HEADER DNA 27-AUG-12 4GSI TITLE DNA HOLLIDAY JUNCTION STABILIZED BY FLUORINE HALOGEN BOND. F2J TITLE 2 CONSTRUCT OF RELATED REFERENCE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3'); COMPND 3 CHAIN: A, C, F, H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3'); COMPND 7 CHAIN: B, D, E, G; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETICALLY ENGINEERED DNA SEQUENCE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHETICALLY ENGINEERED DNA SEQUENCE KEYWDS DNA HOLLIDAY JUNCTION, HALOGEN BOND, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.HO,M.CARTER REVDAT 4 13-SEP-23 4GSI 1 LINK REVDAT 3 15-NOV-17 4GSI 1 REMARK REVDAT 2 18-DEC-13 4GSI 1 JRNL REVDAT 1 31-JUL-13 4GSI 0 JRNL AUTH M.CARTER,A.R.VOTH,M.R.SCHOLFIELD,B.RUMMEL,L.C.SOWERS,P.S.HO JRNL TITL ENTHALPY-ENTROPY COMPENSATION IN BIOMOLECULAR HALOGEN BONDS JRNL TITL 2 MEASURED IN DNA JUNCTIONS. JRNL REF BIOCHEMISTRY V. 52 4891 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23789744 JRNL DOI 10.1021/BI400590H REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 27432.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 74.2 REMARK 3 NUMBER OF REFLECTIONS : 3398 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) : 0.225 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 180 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.022 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.53 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 347 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 31 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.065 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1616 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.48000 REMARK 3 B22 (A**2) : 3.58000 REMARK 3 B33 (A**2) : -6.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.32 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.66 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.002 REMARK 3 BOND ANGLES (DEGREES) : 0.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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 : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 85.88 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 : MCDNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : MCDNA-RNA.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4GSI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 133 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3910 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 24.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 3.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.20700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2ORG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7MM DNA, 25MM SODIUM CACODYLATE PH REMARK 280 7.0 BUFFER, 10-25MM CALCIUM CHLORIDE, AND 0.8-1.2MM SPERMINE, REMARK 280 EQUILIBRATED AGAINST A RESERVOIR OF 30-40% AQUEOUS MPD, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 32.60650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.95850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.60650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.95850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH E 311 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 302 LIES ON A SPECIAL POSITION. 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 O HOH E 306 O HOH E 309 1.92 REMARK 500 O HOH B 103 O HOH G 317 2.01 REMARK 500 OP1 DG F 219 O HOH F 320 2.10 REMARK 500 OP1 DG B 19 O HOH F 320 2.10 REMARK 500 OP2 DG E 210 O HOH E 308 2.12 REMARK 500 OP2 DG A 10 O HOH E 308 2.12 REMARK 500 OP2 DC D 37 O HOH D 102 2.14 REMARK 500 O HOH B 107 O HOH F 318 2.15 REMARK 500 O4' DG F 213 O HOH F 302 2.17 REMARK 500 OP2 DG F 220 O HOH F 301 2.18 REMARK 500 O4' DG B 13 O HOH F 302 2.18 REMARK 500 O HOH G 316 O HOH G 317 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ORG RELATED DB: PDB REMARK 900 RELATED ID: 2ORF RELATED DB: PDB REMARK 900 RELATED ID: 2ORH RELATED DB: PDB REMARK 900 RELATED ID: 3TOK RELATED DB: PDB REMARK 900 RELATED ID: 4GQD RELATED DB: PDB REMARK 900 RELATED ID: 4GRE RELATED DB: PDB REMARK 900 RELATED ID: 4GS2 RELATED DB: PDB REMARK 900 RELATED ID: 4GSG RELATED DB: PDB DBREF 4GSI A 1 10 PDB 4GSI 4GSI 1 10 DBREF 4GSI C 21 30 PDB 4GSI 4GSI 21 30 DBREF 4GSI F 211 220 PDB 4GSI 4GSI 211 220 DBREF 4GSI H 231 240 PDB 4GSI 4GSI 231 240 DBREF 4GSI B 11 20 PDB 4GSI 4GSI 11 20 DBREF 4GSI D 31 40 PDB 4GSI 4GSI 31 40 DBREF 4GSI E 201 210 PDB 4GSI 4GSI 201 210 DBREF 4GSI G 221 230 PDB 4GSI 4GSI 221 230 SEQRES 1 A 10 DC DC DG DG DT DA UFP DC DG DG SEQRES 1 B 10 DC DC DG DA DT DA DC DC DG DG SEQRES 1 C 10 DC DC DG DG DT DA UFP DC DG DG SEQRES 1 D 10 DC DC DG DA DT DA DC DC DG DG SEQRES 1 E 10 DC DC DG DA DT DA DC DC DG DG SEQRES 1 F 10 DC DC DG DG DT DA UFP DC DG DG SEQRES 1 G 10 DC DC DG DA DT DA DC DC DG DG SEQRES 1 H 10 DC DC DG DG DT DA UFP DC DG DG HET UFP A 7 20 HET UFP C 27 20 HET UFP F 217 20 HET UFP H 237 20 HETNAM UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE FORMUL 1 UFP 4(C9 H12 F N2 O8 P) FORMUL 9 HOH *100(H2 O) LINK O3'A DA A 6 P AUFP A 7 1555 1555 1.61 LINK O3'AUFP A 7 P A DC A 8 1555 1555 1.60 LINK O3'A DA C 26 P AUFP C 27 1555 1555 1.61 LINK O3'AUFP C 27 P A DC C 28 1555 1555 1.61 LINK O3'B DA F 216 P BUFP F 217 1555 1555 1.60 LINK O3'BUFP F 217 P B DC F 218 1555 1555 1.60 LINK O3'B DA H 236 P BUFP H 237 1555 1555 1.61 LINK O3'BUFP H 237 P B DC H 238 1555 1555 1.60 CRYST1 65.213 23.917 77.450 90.00 114.80 90.00 C 1 2 1 16 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 0.015334 0.000000 0.007086 0.00000 SCALE2 0.000000 0.041811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014223 0.00000