HEADER DNA 16-FEB-25 9NCH TITLE [6,7,6,P-2] SHIFTED TENSEGRITY TRIANGLE WITH AN (ARM,CENTER,ARM) TITLE 2 DISTRIBUTION OF (6,7,6) BASE PAIRS, 2 NT STICKY ENDS, AND 5' TITLE 3 PHOSPHATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3'); COMPND 15 CHAIN: D; COMPND 16 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; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS TENSEGRITY TRIANGLE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR A.HORVATH,S.VECCHIONI,K.WOLOSZYN,Y.P.OHAYON,R.SHA REVDAT 1 26-MAR-25 9NCH 0 JRNL AUTH A.HORVATH,S.VECCHIONI,K.WOLOSZYN,Y.P.OHAYON,R.SHA JRNL TITL SHIFTED TENSEGRITY TRIANGLES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.8 REMARK 3 NUMBER OF REFLECTIONS : 2386 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.271 REMARK 3 R VALUE (WORKING SET) : 0.270 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 119 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 32.8600 - 4.0000 0.73 2267 119 0.2699 0.2993 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.517 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 233.6 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 213.0 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 : 0.006 962 REMARK 3 ANGLE : 0.900 1475 REMARK 3 CHIRALITY : 0.045 168 REMARK 3 PLANARITY : 0.003 42 REMARK 3 DIHEDRAL : 42.258 408 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 101 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3451 15.9242 1.3073 REMARK 3 T TENSOR REMARK 3 T11: 2.7314 T22: 2.1453 REMARK 3 T33: 2.2576 T12: -0.5113 REMARK 3 T13: -0.0771 T23: 0.7374 REMARK 3 L TENSOR REMARK 3 L11: 9.0126 L22: 2.2043 REMARK 3 L33: 2.0264 L12: -2.3516 REMARK 3 L13: 3.9056 L23: -0.1049 REMARK 3 S TENSOR REMARK 3 S11: -3.0721 S12: 2.4839 S13: 3.5129 REMARK 3 S21: -1.7288 S22: 2.8544 S23: -1.5710 REMARK 3 S31: -1.2584 S32: -0.7257 S33: -0.8193 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 105 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6021 12.6680 10.4015 REMARK 3 T TENSOR REMARK 3 T11: 2.5407 T22: 0.9018 REMARK 3 T33: 0.6053 T12: 0.3723 REMARK 3 T13: 0.6663 T23: 0.2939 REMARK 3 L TENSOR REMARK 3 L11: 6.7156 L22: 2.0601 REMARK 3 L33: 1.9345 L12: -2.7466 REMARK 3 L13: 2.7802 L23: 1.7208 REMARK 3 S TENSOR REMARK 3 S11: 2.4727 S12: -0.1725 S13: 1.3188 REMARK 3 S21: -1.3567 S22: 0.7906 S23: -1.0103 REMARK 3 S31: -2.1324 S32: 1.1671 S33: 10.0145 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 101 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1886 21.0988 12.6346 REMARK 3 T TENSOR REMARK 3 T11: 0.9187 T22: 1.2240 REMARK 3 T33: 1.8461 T12: 0.8865 REMARK 3 T13: 2.2128 T23: 0.2723 REMARK 3 L TENSOR REMARK 3 L11: 8.0089 L22: 7.0180 REMARK 3 L33: 3.9343 L12: 1.8690 REMARK 3 L13: -0.7840 L23: -1.5318 REMARK 3 S TENSOR REMARK 3 S11: -0.6773 S12: -2.4368 S13: 2.4185 REMARK 3 S21: -0.1704 S22: 2.9737 S23: 2.4386 REMARK 3 S31: -1.8478 S32: -1.7492 S33: 8.1664 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 113 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8534 19.2521 18.1137 REMARK 3 T TENSOR REMARK 3 T11: 1.9298 T22: 1.8619 REMARK 3 T33: 1.7595 T12: 0.0083 REMARK 3 T13: 0.8338 T23: -0.0786 REMARK 3 L TENSOR REMARK 3 L11: 0.6025 L22: 3.6793 REMARK 3 L33: 0.6161 L12: -0.4717 REMARK 3 L13: -0.1898 L23: 1.4825 REMARK 3 S TENSOR REMARK 3 S11: 0.9603 S12: -2.9826 S13: 0.2027 REMARK 3 S21: -0.3896 S22: 1.5801 S23: -2.0131 REMARK 3 S31: -1.7484 S32: 0.8992 S33: 0.6495 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 9NCH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293066. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.991870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2398 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.000 REMARK 200 RESOLUTION RANGE LOW (A) : 64.624 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.29 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MOPS, 1.25 M MAGNESIUM SULFATE, REMARK 280 VAPOR 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -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 53.96250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.15526 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.81667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 53.96250 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 31.15526 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.81667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 53.96250 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 31.15526 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.81667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.31053 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 59.63333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 62.31053 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 59.63333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 62.31053 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 59.63333 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG A 101 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA A 102 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 107 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT A 111 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT C 103 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 104 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9NCH A 101 112 PDB 9NCH 9NCH 101 112 DBREF 9NCH B 105 111 PDB 9NCH 9NCH 105 111 DBREF 9NCH C 101 114 PDB 9NCH 9NCH 101 114 DBREF 9NCH D 113 121 PDB 9NCH 9NCH 113 121 SEQRES 1 A 12 DG DA DG DC DA DG DC DC DT DG DT DA SEQRES 1 B 7 DA DC DA DC DC DG DT SEQRES 1 C 14 DT DC DT DG DA DT DG DT DG DG DC DT DG SEQRES 2 C 14 DC SEQRES 1 D 9 DC DG DG DA DC DA DT DC DA CRYST1 107.925 107.925 89.450 90.00 90.00 120.00 H 3 9 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 0.009266 0.005350 0.000000 0.00000 SCALE2 0.000000 0.010699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011179 0.00000 MASTER 299 0 0 0 0 0 0 6 861 4 0 5 END