HEADER DNA 21-MAY-19 6RSP TITLE L-[RU(PHEN)2(11-NO2-DPPZ)]2+ BOUND TO THE OLIGONUCLEOTIDE SEQUENCE TITLE 2 D(TCGGCGCCGA) 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 2 15-MAY-24 6RSP 1 LINK REVDAT 1 08-JUL-20 6RSP 0 JRNL AUTH K.T.MCQUAID,J.P.HALL,C.J.CARDIN JRNL TITL L-[RU(PHEN)2(11-NO2-DPPZ)]2+ BOUND TO THE OLIGONUCLEOTIDE JRNL TITL 2 SEQUENCE D(TCGGCGCCGA) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15RC2_3433: ???) 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 10800 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) : 0.186 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 504 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 33.3152 - 3.0314 1.00 2570 142 0.1691 0.2016 REMARK 3 2 3.0314 - 2.4063 1.00 2556 152 0.2206 0.2057 REMARK 3 3 2.4063 - 2.1022 1.00 2615 105 0.1990 0.2588 REMARK 3 4 2.1022 - 1.9100 1.00 2555 105 0.2624 0.3290 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.660 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 : 0.012 720 REMARK 3 ANGLE : 1.225 1150 REMARK 3 CHIRALITY : 0.054 78 REMARK 3 PLANARITY : 0.012 36 REMARK 3 DIHEDRAL : 26.880 216 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): 11.6359 -10.7659 3.1375 REMARK 3 T TENSOR REMARK 3 T11: 0.3195 T22: 0.4910 REMARK 3 T33: 0.4228 T12: -0.0351 REMARK 3 T13: 0.0143 T23: 0.0190 REMARK 3 L TENSOR REMARK 3 L11: 5.8212 L22: 6.3581 REMARK 3 L33: 6.7258 L12: -4.6120 REMARK 3 L13: -5.3014 L23: 2.4192 REMARK 3 S TENSOR REMARK 3 S11: -0.0232 S12: -0.6577 S13: 0.0040 REMARK 3 S21: 0.2633 S22: -0.0206 S23: 0.0762 REMARK 3 S31: 0.1232 S32: -0.0822 S33: 0.0985 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7851 -11.9250 -4.1250 REMARK 3 T TENSOR REMARK 3 T11: 0.4660 T22: 0.3239 REMARK 3 T33: 0.4144 T12: -0.0130 REMARK 3 T13: -0.0341 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 6.1661 L22: 6.7086 REMARK 3 L33: 7.0348 L12: -4.2725 REMARK 3 L13: -3.1812 L23: 5.5777 REMARK 3 S TENSOR REMARK 3 S11: -0.0997 S12: 0.1949 S13: -0.3128 REMARK 3 S21: -0.6549 S22: -0.0288 S23: 0.1202 REMARK 3 S31: -0.0123 S32: -0.0078 S33: 0.0366 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 6RSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-19 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5650 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 33.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RED RHOMBOHEDRA REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8 UL DROP CONTAINING; 250 UM REMARK 280 D(TCGGCGCCGA), 500 UM RAC-[RU(PHEN)2(11-NO2-DPPZ)]CL2, 7.5% V/V REMARK 280 MPD, 30 MM PH 7 SODIUM CACODYLATE, 9 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 60 MM KCL AND 15 MM BACL2, ALL EQUILIBRATED REMARK 280 AGAINST 500 UL OF 35% V/V MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 16.23000 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 24.34500 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 8.11500 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: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 201 O 150.1 REMARK 620 3 HOH A 208 O 64.3 132.3 REMARK 620 4 HOH A 209 O 91.6 117.1 67.9 REMARK 620 5 HOH A 220 O 121.6 77.2 57.8 74.4 REMARK 620 N 1 2 3 4 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 B 203 O 148.7 REMARK 620 3 HOH B 204 O 130.7 60.8 REMARK 620 4 HOH B 209 O 61.7 131.5 142.0 REMARK 620 5 HOH B 214 O 96.2 114.7 71.4 71.4 REMARK 620 6 HOH B 221 O 129.8 69.8 91.6 68.2 69.9 REMARK 620 N 1 2 3 4 5 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 KHK 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 KHK B 102 DBREF 6RSP A 1 10 PDB 6RSP 6RSP 1 10 DBREF 6RSP B 1 10 PDB 6RSP 6RSP 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 KHK A 102 158 HET BA B 101 1 HET KHK B 102 158 HETNAM BA BARIUM ION HETNAM KHK RUTHENIUM (BIS-(PHENANTHROLINE)) (11-NITRO- HETNAM 2 KHK DIPYRIDOPHENAZINE) FORMUL 3 BA 2(BA 2+) FORMUL 4 KHK 2(C42 H25 N9 O2 RU) FORMUL 7 HOH *41(H2 O) LINK O6 DG A 4 BA BA A 101 1555 1555 2.74 LINK BA BA A 101 O HOH A 201 1555 1555 2.60 LINK BA BA A 101 O HOH A 208 1555 1555 2.63 LINK BA BA A 101 O HOH A 209 1555 1555 2.73 LINK BA BA A 101 O HOH A 220 1555 1555 2.67 LINK O6 DG B 4 BA BA B 101 1555 1555 2.78 LINK BA BA B 101 O HOH B 203 1555 1555 2.63 LINK BA BA B 101 O HOH B 204 1555 1555 2.58 LINK BA BA B 101 O HOH B 209 1555 1555 2.69 LINK BA BA B 101 O HOH B 214 1555 1555 2.80 LINK BA BA B 101 O HOH B 221 1555 1555 2.53 SITE 1 AC1 8 DG A 3 DG A 4 HOH A 201 HOH A 203 SITE 2 AC1 8 HOH A 208 HOH A 209 HOH A 210 HOH A 220 SITE 1 AC2 9 DC A 7 DC A 8 DG A 9 DA A 10 SITE 2 AC2 9 DT B 1 DC B 2 DG B 3 DG B 4 SITE 3 AC2 9 DC B 5 SITE 1 AC3 8 DG B 3 DG B 4 HOH B 203 HOH B 204 SITE 2 AC3 8 HOH B 209 HOH B 212 HOH B 214 HOH B 221 SITE 1 AC4 8 DT A 1 DC A 2 DG A 3 DG A 4 SITE 2 AC4 8 DC B 7 DC B 8 DG B 9 DA B 10 CRYST1 47.108 47.108 32.460 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 0.021228 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021228 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030807 0.00000