HEADER DNA 11-OCT-18 6HWG TITLE [RU(PHEN)2(DPPZ-11-CN)]2+ BOUND TO D(TCGGCGCCGA)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-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 RUTHENIUM, INTERCALATION, DNA, ASYMMETRIC EXPDTA X-RAY DIFFRACTION AUTHOR K.T.MCQUAID,J.P.HALL,C.J.CARDIN REVDAT 1 30-OCT-19 6HWG 0 JRNL AUTH K.T.MCQUAID,J.P.HALL,C.J.CARDIN JRNL TITL [RU(PHEN)2(DPPZ-11-CN)]2+ BOUND TO D(TCGGCGCCGA)2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.9021 - 3.1620 1.00 2438 124 0.1505 0.1314 REMARK 3 2 3.1620 - 2.5100 1.00 2428 127 0.1968 0.2598 REMARK 3 3 2.5100 - 2.1928 1.00 2440 118 0.2049 0.2569 REMARK 3 4 2.1928 - 1.9923 1.00 2348 163 0.2465 0.2908 REMARK 3 5 1.9923 - 1.8495 0.99 2444 134 0.3077 0.3099 REMARK 3 6 1.8495 - 1.7405 1.00 2441 133 0.3398 0.3303 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.59 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 650 REMARK 3 ANGLE : 1.385 1030 REMARK 3 CHIRALITY : 0.065 87 REMARK 3 PLANARITY : 0.012 29 REMARK 3 DIHEDRAL : 26.501 207 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5943 -12.4174 5.0311 REMARK 3 T TENSOR REMARK 3 T11: 0.3311 T22: 0.3623 REMARK 3 T33: 0.3075 T12: -0.0978 REMARK 3 T13: 0.0427 T23: -0.0381 REMARK 3 L TENSOR REMARK 3 L11: 5.5622 L22: 5.8336 REMARK 3 L33: 2.0653 L12: -3.0829 REMARK 3 L13: 3.4695 L23: -2.2901 REMARK 3 S TENSOR REMARK 3 S11: -0.0288 S12: -0.0461 S13: -0.1485 REMARK 3 S21: 0.5708 S22: 0.1425 S23: 0.2434 REMARK 3 S31: -0.3797 S32: -0.2368 S33: -0.0576 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6029 -11.3734 -1.9733 REMARK 3 T TENSOR REMARK 3 T11: 0.3824 T22: 0.2883 REMARK 3 T33: 0.3157 T12: -0.0887 REMARK 3 T13: 0.0210 T23: -0.0490 REMARK 3 L TENSOR REMARK 3 L11: 5.9534 L22: 4.8633 REMARK 3 L33: 2.9995 L12: -3.8042 REMARK 3 L13: 2.7739 L23: -3.8228 REMARK 3 S TENSOR REMARK 3 S11: 0.1366 S12: 0.4401 S13: -0.2694 REMARK 3 S21: -0.0932 S22: -0.0006 S23: 0.2501 REMARK 3 S31: 0.1273 S32: 0.3315 S33: -0.1661 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HWG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012394. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : DUAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7989 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 33.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.03763 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.35800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1UL 1MM DSDNA, 1UL 3MM L REMARK 280 -[RU(PHEN)2(DPPZ-11-CN)]2+, 6UL OF A SOLUTION CONTAINING 10% (V/ REMARK 280 V) 2-METHYL-2,4-PENTANEDIOL, 80MM NACL, 20MM NA-CACODYLATE PH 7, REMARK 280 20MM BACL2 AND 12MM SPERMINE TETRA-HCL EQUILIBRATED AGAINST REMARK 280 500UL 35% 2-METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 16.81600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.22400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.40800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 101 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 O6 REMARK 620 2 HOH A 203 O 67.7 REMARK 620 3 HOH A 240 O 125.5 81.2 REMARK 620 4 HOH B 213 O 64.8 80.9 66.9 REMARK 620 5 HOH A 218 O 140.6 81.4 69.7 135.0 REMARK 620 6 HOH A 221 O 126.2 144.4 105.3 134.2 69.1 REMARK 620 7 HOH A 235 O 112.6 143.7 69.5 68.3 106.8 67.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 101 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 4 O6 REMARK 620 2 HOH A 212 O 65.7 REMARK 620 3 HOH B 235 O 114.5 68.3 REMARK 620 4 HOH B 217 O 126.7 129.9 62.9 REMARK 620 5 HOH B 205 O 66.7 80.1 142.4 149.3 REMARK 620 6 HOH B 242 O 124.9 66.7 69.8 104.7 79.5 REMARK 620 7 HOH B 212 O 140.5 134.0 105.0 71.7 82.3 68.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GWQ A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GWQ B 102 DBREF 6HWG A 1 10 PDB 6HWG 6HWG 1 10 DBREF 6HWG B 1 10 PDB 6HWG 6HWG 1 10 SEQRES 1 A 10 DT DC DG DG DC DG DC DC DG DA SEQRES 1 B 10 DT DC DG DG DC DG DC DC DG DA HET BA A 101 1 HET GWQ A 102 53 HET BA B 101 1 HET GWQ B 102 53 HETNAM BA BARIUM ION HETNAM GWQ RUTHENIUM (BIS-(PHENANTHROLINE)) (11-CYANO- HETNAM 2 GWQ DIPYRIDOPHENAZINE) FORMUL 3 BA 2(BA 2+) FORMUL 4 GWQ 2(C43 H25 N9 RU 2+) FORMUL 7 HOH *83(H2 O) LINK O6 DG A 4 BA BA A 101 1555 1555 2.88 LINK O6 DG B 4 BA BA B 101 1555 1555 2.87 LINK BA BA A 101 O HOH A 203 1555 1555 2.80 LINK BA BA A 101 O HOH A 240 1555 1555 2.78 LINK BA BA A 101 O HOH B 213 1555 1555 2.90 LINK BA BA A 101 O HOH A 218 1555 1555 2.84 LINK BA BA A 101 O HOH A 221 1555 1555 2.79 LINK BA BA A 101 O HOH A 235 1555 1555 2.89 LINK BA BA B 101 O HOH A 212 1555 1555 2.97 LINK BA BA B 101 O HOH B 235 1555 1555 2.92 LINK BA BA B 101 O HOH B 217 1555 1555 2.82 LINK BA BA B 101 O HOH B 205 1555 1555 2.70 LINK BA BA B 101 O HOH B 242 1555 1555 2.72 LINK BA BA B 101 O HOH B 212 1555 1555 2.94 SITE 1 AC1 8 DG A 3 DG A 4 HOH A 203 HOH A 218 SITE 2 AC1 8 HOH A 221 HOH A 235 HOH A 240 HOH B 213 SITE 1 AC2 8 DC A 7 DC A 8 DG A 9 DA A 10 SITE 2 AC2 8 DT B 1 DC B 2 DG B 3 DG B 4 SITE 1 AC3 8 HOH A 212 DG B 3 DG B 4 HOH B 205 SITE 2 AC3 8 HOH B 212 HOH B 217 HOH B 235 HOH B 242 SITE 1 AC4 10 DT A 1 DC A 2 DG A 3 DG A 4 SITE 2 AC4 10 DC B 7 DC B 8 DG B 9 DA B 10 SITE 3 AC4 10 HOH B 204 HOH B 216 CRYST1 47.936 47.936 33.632 90.00 90.00 90.00 P 43 8 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 0.020861 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029734 0.00000