HEADER DNA 29-MAY-18 6GN2 TITLE RACEMIC CRYSTAL STRUCTURE OF A-DNA DUPLEX FORMED FROM D(CCCGGG) IN TITLE 2 SPACE GROUP R3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RACEMATE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC REVDAT 2 17-JAN-24 6GN2 1 REMARK REVDAT 1 11-SEP-19 6GN2 0 JRNL AUTH P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC JRNL TITL RACEMIC CRYSTAL STRUCTURES OF A-DNA DUPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC REMARK 1 TITL RACEMIC DNA CRYSTALLOGRAPHY REMARK 1 REF ANGEW. CHEM. INT. ED. V. 53 14424 2014 REMARK 1 REFN ISSN 1433-7851 REMARK 1 PMID 25358289 REMARK 1 DOI 10.1002/ANIE.201409014 REMARK 2 REMARK 2 RESOLUTION. 2.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 7997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.260 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.120 REMARK 3 FREE R VALUE TEST SET COUNT : 809 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 26.3547 - 4.5004 0.97 1203 133 0.2142 0.2006 REMARK 3 2 4.5004 - 3.5750 0.98 1204 136 0.2174 0.2127 REMARK 3 3 3.5750 - 3.1239 0.97 1203 141 0.2407 0.3056 REMARK 3 4 3.1239 - 2.8386 0.99 1220 132 0.3139 0.3638 REMARK 3 5 2.8386 - 2.6354 0.99 1232 142 0.3964 0.3384 REMARK 3 6 2.6354 - 2.4801 0.92 1126 125 0.3732 0.4340 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.27 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 : 0.003 544 REMARK 3 ANGLE : 0.392 832 REMARK 3 CHIRALITY : 0.014 92 REMARK 3 PLANARITY : 0.001 24 REMARK 3 DIHEDRAL : 12.629 224 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 74.5173 74.9924 8.2679 REMARK 3 T TENSOR REMARK 3 T11: 0.4437 T22: 0.1925 REMARK 3 T33: 0.3842 T12: -0.0507 REMARK 3 T13: 0.0411 T23: -0.0832 REMARK 3 L TENSOR REMARK 3 L11: 4.3131 L22: 5.6023 REMARK 3 L33: 9.2047 L12: 3.2099 REMARK 3 L13: -2.6500 L23: -6.9067 REMARK 3 S TENSOR REMARK 3 S11: 0.0389 S12: -0.1294 S13: 0.2700 REMARK 3 S21: -0.2553 S22: 0.0124 S23: -0.0359 REMARK 3 S31: -1.4908 S32: 0.1454 S33: -0.1468 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.1916 68.1949 10.3815 REMARK 3 T TENSOR REMARK 3 T11: 0.3618 T22: 0.1782 REMARK 3 T33: 0.3914 T12: -0.0399 REMARK 3 T13: 0.0233 T23: -0.0325 REMARK 3 L TENSOR REMARK 3 L11: 2.2208 L22: 0.0662 REMARK 3 L33: 9.2950 L12: 0.0271 REMARK 3 L13: 2.8030 L23: 0.6666 REMARK 3 S TENSOR REMARK 3 S11: 0.0770 S12: 0.0009 S13: -0.0888 REMARK 3 S21: 0.1816 S22: 0.2219 S23: -0.3115 REMARK 3 S31: -0.1253 S32: 0.3125 S33: -0.3738 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 81.8448 66.5355 -3.8721 REMARK 3 T TENSOR REMARK 3 T11: 0.2497 T22: 0.2815 REMARK 3 T33: 0.3437 T12: 0.0803 REMARK 3 T13: 0.0037 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 4.0468 L22: 7.1175 REMARK 3 L33: 2.9621 L12: 3.2967 REMARK 3 L13: -0.9170 L23: -2.2219 REMARK 3 S TENSOR REMARK 3 S11: 0.1769 S12: 0.2998 S13: -0.1224 REMARK 3 S21: 0.1765 S22: -0.3185 S23: -0.5570 REMARK 3 S31: -0.0930 S32: 0.2951 S33: 0.1030 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 75.9145 66.6237 -7.8107 REMARK 3 T TENSOR REMARK 3 T11: 0.3253 T22: 0.1978 REMARK 3 T33: 0.2741 T12: 0.0643 REMARK 3 T13: 0.0146 T23: 0.0512 REMARK 3 L TENSOR REMARK 3 L11: 3.2198 L22: 9.7179 REMARK 3 L33: 5.7215 L12: -3.1265 REMARK 3 L13: -2.6992 L23: 7.2767 REMARK 3 S TENSOR REMARK 3 S11: 0.3032 S12: 0.2826 S13: 0.2683 REMARK 3 S21: -0.9078 S22: -0.1933 S23: 0.0704 REMARK 3 S31: -0.8040 S32: -0.1752 S33: -0.0834 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 6GN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1200010268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5417 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8101 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 23.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.05740 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42490 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.020 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1VT5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H -3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,-Z REMARK 290 5555 Y,-X+Y,-Z REMARK 290 6555 X-Y,X,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 -X+2/3,-Y+1/3,-Z+1/3 REMARK 290 11555 Y+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 12555 X-Y+2/3,X+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 -X+1/3,-Y+2/3,-Z+2/3 REMARK 290 17555 Y+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 18555 X-Y+1/3,X+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 52.70650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.43011 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 18.71033 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 52.70650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.43011 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 18.71033 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 52.70650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.43011 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 18.71033 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 52.70650 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 30.43011 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 18.71033 REMARK 290 SMTRY1 11 0.500000 0.866025 0.000000 52.70650 REMARK 290 SMTRY2 11 -0.866025 0.500000 0.000000 30.43011 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 18.71033 REMARK 290 SMTRY1 12 0.500000 -0.866025 0.000000 52.70650 REMARK 290 SMTRY2 12 0.866025 0.500000 0.000000 30.43011 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 18.71033 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 60.86022 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 37.42067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 60.86022 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 37.42067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 60.86022 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 37.42067 REMARK 290 SMTRY1 16 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 60.86022 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 37.42067 REMARK 290 SMTRY1 17 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 17 -0.866025 0.500000 0.000000 60.86022 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 37.42067 REMARK 290 SMTRY1 18 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 0.866025 0.500000 0.000000 60.86022 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 37.42067 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 DBREF 6GN2 A 1 6 PDB 6GN2 6GN2 1 6 DBREF 6GN2 B 7 12 PDB 6GN2 6GN2 7 12 DBREF 6GN2 C 1 6 PDB 6GN2 6GN2 1 6 DBREF 6GN2 D 7 12 PDB 6GN2 6GN2 7 12 SEQRES 1 A 6 DC DC DC DG DG DG SEQRES 1 B 6 DC DC DC DG DG DG SEQRES 1 C 6 DC DC DC DG DG DG SEQRES 1 D 6 DC DC DC DG DG DG HET TMO B 101 5 HET TMO B 102 5 HETNAM TMO TRIMETHYLAMINE OXIDE FORMUL 5 TMO 2(C3 H9 N O) FORMUL 7 HOH *49(H2 O) CRYST1 105.413 105.413 56.131 90.00 90.00 120.00 H -3 72 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 0.009486 0.005477 0.000000 0.00000 SCALE2 0.000000 0.010954 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017815 0.00000