HEADER DNA 22-SEP-14 4RE7 TITLE LAMBDA-[RU(TAP)2(DPPZ)]2+ BOUND TO D(TCIGCGCCGA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*CP*IP*GP*CP*GP*CP*CP*GP*A)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS INOSINE, KINKING, RUTHENIUM, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.P.HALL,C.J.CARDIN REVDAT 3 28-FEB-24 4RE7 1 REMARK LINK REVDAT 2 22-NOV-17 4RE7 1 REMARK REVDAT 1 30-SEP-15 4RE7 0 JRNL AUTH J.P.HALL,S.P.GURUNG,H.BEER,K.BUCHNER,D.J.CARDIN,J.A.BRAZIER, JRNL AUTH 2 C.J.CARDIN JRNL TITL THE EFFECTS OF DNA MODIFICATION ON THE BINDING OF JRNL TITL 2 POLYPYRIDYL RUTHENIUM COMPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 2000 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) : 0.193 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.570 REMARK 3 FREE R VALUE TEST SET COUNT : 159 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 33.8250 - 2.1810 0.93 3318 159 0.1925 0.2417 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 45.480 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 : 0.005 289 REMARK 3 ANGLE : 1.915 454 REMARK 3 CHIRALITY : 0.027 38 REMARK 3 PLANARITY : 0.002 13 REMARK 3 DIHEDRAL : 28.048 97 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): 10.5399 11.9227 -19.6956 REMARK 3 T TENSOR REMARK 3 T11: 0.7892 T22: 0.7835 REMARK 3 T33: 0.5859 T12: 0.0531 REMARK 3 T13: -0.0091 T23: -0.0285 REMARK 3 L TENSOR REMARK 3 L11: 4.9133 L22: 6.1569 REMARK 3 L33: 1.8969 L12: -2.1317 REMARK 3 L13: 2.0699 L23: -2.6301 REMARK 3 S TENSOR REMARK 3 S11: -0.0704 S12: 0.2214 S13: -0.7320 REMARK 3 S21: -0.3011 S22: 0.2186 S23: 0.1891 REMARK 3 S31: -0.2632 S32: -0.1487 S33: -0.0333 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 4RE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-14 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 47.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 1.12200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 59.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 UL 2 MM OLIGONUCLEOTIDE (DOUBLE HPLC REMARK 280 -PURIFIED) + 1 UL 2 MM LAMBDA-[RU(TAP)2(DPPZ)]CL2 + 6 UL 10% V/V REMARK 280 MPD, 40 MM SODIUM CACODYLATE, PH 6.0, 12 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 80 MM SODIUM CHLORIDE, 20 MM BARIUM CHLORIDE REMARK 280 EQUILIBRATED AGAINST 1 ML 35% V/V MPD, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K, PH 7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 16.05500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.91500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.08250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.91500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.91500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.02750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.91500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.91500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.08250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.91500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.91500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 8.02750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 16.05500 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: 1930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -32.11000 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 DI A 3 N7 REMARK 620 2 DG A 4 O6 75.2 REMARK 620 N 1 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 RKL A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QRN RELATED DB: PDB REMARK 900 LAMBDA-[RU(TAP)2(DPPZ)]2+ BOUND TO D(TCGGCGCCGA) REMARK 900 RELATED ID: 4QIO RELATED DB: PDB REMARK 900 LAMBDA-[RU(TAP)2(DPPZ)]2+ BOUND TO D(TCGGCGCCIA) DBREF 4RE7 A 1 10 PDB 4RE7 4RE7 1 10 SEQRES 1 A 10 DT DC DI DG DC DG DC DC DG DA HET BA A 101 1 HET RKL A 102 51 HETNAM BA BARIUM ION HETNAM RKL RU(TAP)2(DPPZ) COMPLEX FORMUL 2 BA BA 2+ FORMUL 3 RKL C38 H22 N12 RU 2+ FORMUL 4 HOH *(H2 O) LINK N7 DI A 3 BA BA A 101 1555 1555 2.91 LINK O6 DG A 4 BA BA A 101 1555 1555 2.80 SITE 1 AC1 2 DI A 3 DG A 4 SITE 1 AC2 8 DT A 1 DC A 2 DI A 3 DG A 4 SITE 2 AC2 8 DC A 7 DC A 8 DG A 9 DA A 10 CRYST1 47.830 47.830 32.110 90.00 90.00 90.00 P 43 21 2 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 0.020907 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031143 0.00000