PDB Short entry for 1WQZ HEADER DNA 07-OCT-04 1WQZ TITLE COMPLICATED WATER ORIENTATIONS IN THE MINOR GROOVE OF B-DNA DECAMER TITLE 2 D(CCATTAATGG)2 OBSERVED BY NEUTRON DIFFRACTION MEASUREMENTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS B-DNA, HYDRATION, HYDROGEN, DNA EXPDTA NEUTRON DIFFRACTION AUTHOR S.ARAI,T.CHATAKE,T.OHHARA,K.KURIHARA,I.TANAKA,N.SUZUKI,Z.FUJIMOTO, AUTHOR 2 H.MIZUNO,N.NIIMURA REVDAT 7 25-OCT-23 1WQZ 1 REMARK REVDAT 6 04-JUL-18 1WQZ 1 SOURCE REMARK REVDAT 5 07-MAR-18 1WQZ 1 REMARK REVDAT 4 13-JUL-11 1WQZ 1 VERSN REVDAT 3 24-FEB-09 1WQZ 1 VERSN REVDAT 2 05-JUN-07 1WQZ 1 REMARK REVDAT 1 21-JUN-05 1WQZ 0 JRNL AUTH S.ARAI,T.CHATAKE,T.OHHARA,K.KURIHARA,I.TANAKA,N.SUZUKI, JRNL AUTH 2 Z.FUJIMOTO,H.MIZUNO,N.NIIMURA JRNL TITL COMPLICATED WATER ORIENTATIONS IN THE MINOR GROOVE OF THE JRNL TITL 2 B-DNA DECAMER D(CCATTAATGG)2 OBSERVED BY NEUTRON DIFFRACTION JRNL TITL 3 MEASUREMENTS JRNL REF NUCLEIC ACIDS RES. V. 33 3017 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 15914673 JRNL DOI 10.1093/NAR/GKI616 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 63.4 REMARK 3 NUMBER OF REFLECTIONS : 879 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) : 0.252 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 79 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 100 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.26 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 8 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 : 404 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.00 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.16 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : -0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 BOND ANGLES (DEGREES) : 1.060 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 0.000 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.160 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1WQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000023896. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 17-MAY-03 REMARK 230 TEMPERATURE (KELVIN) : 279.0 REMARK 230 PH : 7.00 REMARK 230 NUMBER OF CRYSTALS USED : 2 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 1G-A REMARK 230 WAVELENGTH OR RANGE (A) : 2.60 REMARK 230 MONOCHROMATOR : ELASTICALLY-BENT PERFECT SILICON REMARK 230 MONOCHROMATOR REMARK 230 OPTICS : JAERI BIX-4 REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : NULL REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 230 DATA SCALING SOFTWARE : SCALEPACK REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 896 REMARK 230 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 230 RESOLUTION RANGE LOW (A) : 100.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 63.1 REMARK 230 DATA REDUNDANCY : 1.230 REMARK 230 R MERGE (I) : 0.23300 REMARK 230 R SYM (I) : NULL REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : 5.8030 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 230 COMPLETENESS FOR SHELL (%) : 62.4 REMARK 230 DATA REDUNDANCY IN SHELL : 1.20 REMARK 230 R MERGE FOR SHELL (I) : 0.24500 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 <I/SIGMA(I)> FOR SHELL : 3.633 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : CNS REMARK 230 STARTING MODEL: PDB ENTRY 1WQY REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% MPD, 0.1M MAGNESIUM CHLORIDE, 0.1M REMARK 280 SODIUM CACODYLATE, 0.002M DNA, PD 6.6, PH 7.0, BATCH (D2O), REMARK 280 TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.06667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.03333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.03333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.06667 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, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 D1 DOD B 29 O DOD B 30 1.47 REMARK 500 OP2 DA B 17 D2 DOD B 21 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC A 1 0.07 SIDE CHAIN REMARK 500 DC B 11 0.07 SIDE CHAIN REMARK 500 DT B 15 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WQY RELATED DB: PDB REMARK 900 X-RAY DIFFRACTION DBREF 1WQZ A 1 10 PDB 1WQZ 1WQZ 1 10 DBREF 1WQZ B 11 20 PDB 1WQZ 1WQZ 11 20 SEQRES 1 A 10 DC DC DA DT DT DA DA DT DG DG SEQRES 1 B 10 DC DC DA DT DT DA DA DT DG DG FORMUL 3 DOD *27(D2 O) CRYST1 32.900 32.900 96.100 90.00 90.00 120.00 P 32 2 1 12 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 0.030395 0.017549 0.000000 0.00000 SCALE2 0.000000 0.035097 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010406 0.00000