PDB Short entry for 413D
HEADER    RNA                                     10-JUL-98   413D              
TITLE     A'-FORM RNA DOUBLE HELIX IN THE SINGLE CRYSTAL STRUCTURE OF           
TITLE    2 R(UGAGCUUCGGCUC)                                                     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: RNA (5'-                                                   
COMPND   3 R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP*UP*C)-3');                       
COMPND   4 CHAIN: A;                                                            
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    A'-RNA, DOUBLE HELIX                                                  
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    Y.TANAKA,S.FUJII,H.HIROAKI,T.SAKATA,T.TANAKA,S.UESUGI,K.-             
AUTHOR   2 I.TOMITA,Y.KYOGOKU                                                   
REVDAT   6   24-FEB-09 413D    1       VERSN                                    
REVDAT   5   01-APR-03 413D    1       JRNL                                     
REVDAT   4   27-NOV-00 413D    5                                                
REVDAT   3   03-AUG-00 413D    1       JRNL                                     
REVDAT   2   26-AUG-98 413D    3       REMARK HETATM CRYST1 FORMUL              
REVDAT   2 2                   3       JRNL                                     
REVDAT   1   10-JUL-98 413D    0                                                
SPRSDE     10-JUL-98 413D      373D                                             
JRNL        AUTH   Y.TANAKA,S.FUJII,H.HIROAKI,T.SAKATA,T.TANAKA,                
JRNL        AUTH 2 S.UESUGI,K.TOMITA,Y.KYOGOKU                                  
JRNL        TITL   A'-FORM RNA DOUBLE HELIX IN THE SINGLE CRYSTAL               
JRNL        TITL 2 STRUCTURE OF R(UGAGCUUCGGCUC).                               
JRNL        REF    NUCLEIC ACIDS RES.            V.  27   949 1999              
JRNL        REFN                   ISSN 0305-1048                               
JRNL        PMID   9927725                                                      
JRNL        DOI    10.1093/NAR/27.4.949                                         
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   S.FUJII,Y.TANAKA,S.UESUGI,T.TANAKA,T.SAKATA,                 
REMARK   1  AUTH 2 H.HIROAKI                                                    
REMARK   1  TITL   CONFORMATIONAL FEATURES OF THE FOUR SUCCESSIVE               
REMARK   1  TITL 2 NON-WATSON-CRICK BASE PAIRS IN RNA DUPLEX                    
REMARK   1  REF    NUCLEIC ACIDS SYMP.SER.       V.  27    63 1992              
REMARK   1  REFN                   ISSN 0261-3166                               
REMARK   1 REFERENCE 2                                                          
REMARK   1  AUTH   S.FUJII,Y.TANAKA,K.-I.TOMITA,T.SAKATA,H.HIROAKI,             
REMARK   1  AUTH 2 T.TANAKA,S.UESUGI                                            
REMARK   1  TITL   MOLECULAR STRUCTURE OF EXTRAORDINARILY STABLE RNA            
REMARK   1  TITL 2 : MODEL BUILDING AND X-RAY ANALYSIS                          
REMARK   1  REF    NUCLEIC ACIDS SYMP.SER.       V.  25   181 1991              
REMARK   1  REFN                   ISSN 0261-3166                               
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.851                                         
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 10.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 1.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 69.3                           
REMARK   3   NUMBER OF REFLECTIONS             : 2743                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.182                           
REMARK   3   FREE R VALUE                     : 0.224                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 9.400                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 258                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL                         
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : NULL                         
REMARK   3   BIN FREE R VALUE                    : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL                         
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 0                                       
REMARK   3   NUCLEIC ACID ATOMS       : 288                                     
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 37                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.005                           
REMARK   3   BOND ANGLES            (DEGREES) : 0.90                            
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : NULL                                      
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 413D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 15-DEC-90                          
REMARK 200  TEMPERATURE           (KELVIN) : 293.00                             
REMARK 200  PH                             : 6.50                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU RU300                       
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : NULL                               
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : DIFFRACTOMETER                     
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU AFC-5R                      
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : RIGAKU                             
REMARK 200  DATA SCALING SOFTWARE          : RIGAKU                             
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 3556                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800                              
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL                               
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 88.0                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: X-PLOR                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 52.66                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1                          
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y,-Z                                                 
REMARK 290       3555   X+1/2,Y+1/2,Z                                           
REMARK 290       4555   -X+1/2,Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       19.24500            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       16.15000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       19.24500            
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       16.15000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC                           
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 375                                                                      
REMARK 375 SPECIAL POSITION                                                     
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
REMARK 375 POSITIONS.                                                           
REMARK 375                                                                      
REMARK 375 ATOM RES CSSEQI                                                      
REMARK 375 O4     U A   1  LIES ON A SPECIAL POSITION.                          
DBREF  413D A    1    13  PDB    413D     413D             1     13             
SEQRES   1 A   13    U   G   A   G   C   U   U   C   G   G   C   U   C          
FORMUL   2  HOH   *37(H2 O)                                                     
CRYST1   38.490   32.300   38.760  90.00 117.56  90.00 C 1 2 1       4          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.025981  0.000000  0.013559        0.00000                         
SCALE2      0.000000  0.030960  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.029102        0.00000