HEADER DNA 09-APR-18 6G8S TITLE [RU(TAP)2(11,12-CN2-DPPZ)]2+ BOUND TO D(CCGGACCCGG/CCGGGTCCGG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*GP*GP*TP*CP*CP*GP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*CP*GP*GP*AP*CP*CP*CP*GP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS RUTHENIUM, INTERCALATION, DNA, ASYMMETRIC EXPDTA X-RAY DIFFRACTION AUTHOR K.T.MCQUAID,J.P.HALL,C.J.CARDIN REVDAT 3 08-MAY-24 6G8S 1 LINK REVDAT 2 28-AUG-19 6G8S 1 JRNL REVDAT 1 24-APR-19 6G8S 0 JRNL AUTH K.MCQUAID,J.P.HALL,J.A.BRAZIER,D.J.CARDIN,C.J.CARDIN JRNL TITL X-RAY CRYSTAL STRUCTURES SHOW DNA STACKING ADVANTAGE OF JRNL TITL 2 TERMINAL NITRILE SUBSTITUTION IN RU-DPPZ COMPLEXES. JRNL REF CHEMISTRY V. 24 15859 2018 JRNL REFN ISSN 0947-6539 JRNL PMID 30063271 JRNL DOI 10.1002/CHEM.201803021 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9018 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.420 REMARK 3 FREE R VALUE TEST SET COUNT : 941 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 23.6258 - 3.1734 1.00 2312 165 0.1483 0.1639 REMARK 3 2 3.1734 - 2.5198 1.00 2337 135 0.1998 0.2438 REMARK 3 3 2.5198 - 2.2015 1.00 2374 127 0.1989 0.2634 REMARK 3 4 2.2015 - 2.0003 1.00 2323 128 0.2307 0.1866 REMARK 3 5 2.0003 - 1.8570 1.00 2366 138 0.2909 0.2722 REMARK 3 6 1.8570 - 1.7476 1.00 2352 118 0.3389 0.4328 REMARK 3 7 1.7476 - 1.6601 1.00 2356 130 0.3962 0.3934 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) : 31.090 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 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 : 0.005 638 REMARK 3 ANGLE : 0.939 1002 REMARK 3 CHIRALITY : 0.045 92 REMARK 3 PLANARITY : 0.004 28 REMARK 3 DIHEDRAL : 27.173 222 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): 14.2545 13.1973 5.5714 REMARK 3 T TENSOR REMARK 3 T11: 0.4526 T22: 0.4765 REMARK 3 T33: 0.3965 T12: 0.0729 REMARK 3 T13: -0.0351 T23: -0.0539 REMARK 3 L TENSOR REMARK 3 L11: 0.9237 L22: 0.5315 REMARK 3 L33: 0.0768 L12: 0.7091 REMARK 3 L13: 0.1605 L23: 0.1115 REMARK 3 S TENSOR REMARK 3 S11: 0.5678 S12: -0.2128 S13: -0.1278 REMARK 3 S21: 0.3363 S22: -0.3987 S23: -0.0998 REMARK 3 S31: 0.4403 S32: -0.2690 S33: 0.0163 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7791 10.8490 -3.4934 REMARK 3 T TENSOR REMARK 3 T11: 0.4214 T22: 0.4491 REMARK 3 T33: 0.3718 T12: 0.0946 REMARK 3 T13: -0.0612 T23: -0.0561 REMARK 3 L TENSOR REMARK 3 L11: 0.2726 L22: 0.7806 REMARK 3 L33: 0.1399 L12: 0.4732 REMARK 3 L13: -0.1935 L23: -0.3204 REMARK 3 S TENSOR REMARK 3 S11: -0.2332 S12: 0.2170 S13: -0.1515 REMARK 3 S21: 0.0845 S22: 0.3835 S23: -0.0782 REMARK 3 S31: -0.1579 S32: 0.3784 S33: 0.0002 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 6G8S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-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 : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : DUAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS, XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 27.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.00 REMARK 200 R MERGE FOR SHELL (I) : 0.90500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLISATION WAS OBSERVED IN A REMARK 280 NUMBER OF CONDITIONS FROM THE NUCLEIC ACID MINI-SCREEN FROM REMARK 280 HAMPTON RESEARCH, WHERE THE BEST DIFFRACTING EXAMPLE CAME FROM A REMARK 280 8UL DROP CONTAINING; 125 UM D(CCGGACCCGG/CCGGGTCCGG)2, 750 UM REMARK 280 RAC-[RU(TAP)2(11,12-CN2-DPPZ)]2+, 7.5% V/V MPD, 30 MM PH 7 REMARK 280 SODIUM CACODYLATE, 9 MM SPERMINE TETRAHYDROCHLORIDE, 60 MM KCL REMARK 280 AND 15 MM BACL2; ALL EQUILIBRATED AGAINST 1 ML OF 35% V/V MPD. REMARK 280 ORANGE/RED RODS GREW FOLLOWING ROUGHLY 3 WEEKS OF INCUBATION AT REMARK 280 291 K., VAPOR DIFFUSION, SITTING DROP 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 16.99050 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 25.48575 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 8.49525 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: 2120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 204 O 67.6 REMARK 620 3 HOH A 208 O 128.7 136.4 REMARK 620 4 HOH A 211 O 138.2 76.9 67.0 REMARK 620 5 HOH A 217 O 80.1 134.0 89.3 141.6 REMARK 620 6 HOH A 237 O 136.4 97.7 90.9 68.1 83.4 REMARK 620 7 HOH B 212 O 76.4 71.3 145.2 112.8 69.9 60.0 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 HOH A 214 O REMARK 620 2 DG B 4 O6 75.5 REMARK 620 3 HOH B 205 O 144.9 130.9 REMARK 620 4 HOH B 208 O 69.9 70.0 135.3 REMARK 620 5 HOH B 211 O 114.4 139.3 63.6 76.8 REMARK 620 6 HOH B 220 O 70.8 80.1 89.6 135.1 140.5 REMARK 620 7 HOH B 231 O 65.7 138.1 81.0 108.6 74.6 72.8 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 EQQ 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 EQQ B 102 DBREF 6G8S A 1 10 PDB 6G8S 6G8S 1 10 DBREF 6G8S B 1 10 PDB 6G8S 6G8S 1 10 SEQRES 1 A 10 DC DC DG DG DG DT DC DC DG DG SEQRES 1 B 10 DC DC DG DG DA DC DC DC DG DG HET BA A 101 1 HET EQQ A 102 55 HET BA B 101 1 HET EQQ B 102 55 HETNAM BA BARIUM ION HETNAM EQQ RUTHENIUM (BIS-(TETRAAZAPHENANTHRENE)) (11,12-DICYANO- HETNAM 2 EQQ DIPYRIDOPHENAZINE) FORMUL 3 BA 2(BA 2+) FORMUL 4 EQQ 2(C40 H20 N14 RU) FORMUL 7 HOH *68(H2 O) LINK O6 DG A 4 BA BA A 101 1555 1555 2.75 LINK BA BA A 101 O HOH A 204 1555 1555 2.67 LINK BA BA A 101 O HOH A 208 1555 1555 2.78 LINK BA BA A 101 O HOH A 211 1555 1555 2.73 LINK BA BA A 101 O HOH A 217 1555 1555 2.96 LINK BA BA A 101 O HOH A 237 1555 1555 2.70 LINK BA BA A 101 O HOH B 212 1555 1555 2.96 LINK O HOH A 214 BA BA B 101 1555 1555 2.98 LINK O6 DG B 4 BA BA B 101 1555 1555 2.76 LINK BA BA B 101 O HOH B 205 1555 1555 2.75 LINK BA BA B 101 O HOH B 208 1555 1555 2.68 LINK BA BA B 101 O HOH B 211 1555 1555 2.79 LINK BA BA B 101 O HOH B 220 1555 1555 2.91 LINK BA BA B 101 O HOH B 231 1555 1555 2.72 SITE 1 AC1 8 DG A 3 DG A 4 HOH A 204 HOH A 208 SITE 2 AC1 8 HOH A 211 HOH A 217 HOH A 237 HOH B 212 SITE 1 AC2 12 DC A 7 DC A 8 DG A 9 DG A 10 SITE 2 AC2 12 HOH A 205 HOH A 212 HOH A 221 DC B 1 SITE 3 AC2 12 DC B 2 DG B 3 DG B 4 HOH B 219 SITE 1 AC3 8 HOH A 214 DG B 3 DG B 4 HOH B 205 SITE 2 AC3 8 HOH B 208 HOH B 211 HOH B 220 HOH B 231 SITE 1 AC4 12 DC A 1 DC A 2 DG A 3 DG A 4 SITE 2 AC4 12 HOH A 232 DC B 7 DC B 8 DG B 9 SITE 3 AC4 12 DG B 10 HOH B 207 HOH B 216 HOH B 217 CRYST1 47.247 47.247 33.981 90.00 90.00 90.00 P 43 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 0.021165 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029428 0.00000