HEADER DNA 04-MAR-25 9NM6 TITLE [3,8,9-1] SHIFTED TENSEGRITY TRIANGLE WITH AN (ARM,CENTER,ARM) TITLE 2 DISTRIBUTION OF (3,8,9) BASE PAIRS AND 1 NT STICKY ENDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*GP*CP*GP*TP*CP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*CP*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*CP*TP*GP*AP*CP*GP*CP*TP*GP*TP*GP*CP*T)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(P*GP*AP*GP*CP*TP*GP*TP*G)-3'); COMPND 15 CHAIN: X; 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 10-SEP-25 9NM6 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. 6.58 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) : 6.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.9 REMARK 3 NUMBER OF REFLECTIONS : 840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.100 REMARK 3 FREE R VALUE TEST SET COUNT : 68 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 43.9800 - 6.5800 0.83 772 68 0.2280 0.2517 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) : 0.818 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.803 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 310.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 618.3 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 : 0.006 956 REMARK 3 ANGLE : 0.801 1467 REMARK 3 CHIRALITY : 0.043 166 REMARK 3 PLANARITY : 0.005 42 REMARK 3 DIHEDRAL : 39.796 406 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 112 THROUGH 124 ) REMARK 3 ORIGIN FOR THE GROUP (A): -60.4061 14.7502 6.2962 REMARK 3 T TENSOR REMARK 3 T11: 10.4548 T22: 5.5226 REMARK 3 T33: 2.4466 T12: 1.6998 REMARK 3 T13: 0.3604 T23: -1.3297 REMARK 3 L TENSOR REMARK 3 L11: 1.4457 L22: 1.8072 REMARK 3 L33: 1.4766 L12: -1.3714 REMARK 3 L13: -1.7450 L23: 1.2151 REMARK 3 S TENSOR REMARK 3 S11: 2.0559 S12: 1.3009 S13: -1.2289 REMARK 3 S21: -0.9912 S22: 3.3181 S23: -0.8926 REMARK 3 S31: 4.1100 S32: 1.5046 S33: 4.0461 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 131 THROUGH 138 ) REMARK 3 ORIGIN FOR THE GROUP (A): -63.7733 24.9237 14.3089 REMARK 3 T TENSOR REMARK 3 T11: 3.2278 T22: 3.4397 REMARK 3 T33: 6.6947 T12: 4.8946 REMARK 3 T13: -3.5265 T23: -1.2723 REMARK 3 L TENSOR REMARK 3 L11: 5.5030 L22: 2.2422 REMARK 3 L33: 3.9247 L12: 0.6918 REMARK 3 L13: -4.5906 L23: -1.1324 REMARK 3 S TENSOR REMARK 3 S11: 0.2431 S12: -2.4398 S13: -0.3488 REMARK 3 S21: -1.2395 S22: -1.2261 S23: 0.7868 REMARK 3 S31: 1.4687 S32: 3.1994 S33: -0.1127 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 199 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): -63.0570 9.9243 8.4717 REMARK 3 T TENSOR REMARK 3 T11: 8.5170 T22: 4.5113 REMARK 3 T33: 5.8304 T12: 0.1812 REMARK 3 T13: 1.3205 T23: -0.0801 REMARK 3 L TENSOR REMARK 3 L11: 8.5058 L22: 0.0272 REMARK 3 L33: 7.9773 L12: 0.8697 REMARK 3 L13: 8.2104 L23: 1.0860 REMARK 3 S TENSOR REMARK 3 S11: -0.9161 S12: 3.6280 S13: -0.3569 REMARK 3 S21: 0.7713 S22: -0.3705 S23: 0.1953 REMARK 3 S31: -3.9766 S32: 5.5378 S33: 14.4418 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'X' AND (RESID 104 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -75.6221 20.8122 21.4811 REMARK 3 T TENSOR REMARK 3 T11: 7.7632 T22: 4.4679 REMARK 3 T33: 5.9769 T12: 0.4025 REMARK 3 T13: -1.6451 T23: -1.6686 REMARK 3 L TENSOR REMARK 3 L11: 3.3923 L22: 3.7592 REMARK 3 L33: 0.0174 L12: 3.6688 REMARK 3 L13: -0.3505 L23: -0.4887 REMARK 3 S TENSOR REMARK 3 S11: 5.0872 S12: -5.5816 S13: -2.0987 REMARK 3 S21: 6.3737 S22: -3.9535 S23: -1.7542 REMARK 3 S31: 2.2407 S32: -4.2956 S33: -2.3341 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 9NM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1000293671. 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 : 848 REMARK 200 RESOLUTION RANGE HIGH (A) : 6.578 REMARK 200 RESOLUTION RANGE LOW (A) : 67.182 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 6.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 7.70 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: P 63 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -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 23.84750 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 23.84750 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 23.84750 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, D, X 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, D, X REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -67.18150 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 116.36177 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, X REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -134.36300 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 DC A 117 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 133 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG D 209 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG X 106 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9NM6 A 112 124 PDB 9NM6 9NM6 112 124 DBREF 9NM6 B 131 138 PDB 9NM6 9NM6 131 138 DBREF 9NM6 D 199 211 PDB 9NM6 9NM6 199 211 DBREF 9NM6 X 104 111 PDB 9NM6 9NM6 104 111 SEQRES 1 A 13 DA DC DG DG DA DC DA DG DC DG DT DC DA SEQRES 1 B 8 DC DA DC DA DC DC DG DT SEQRES 1 D 13 DC DT DG DA DC DG DC DT DG DT DG DC DT SEQRES 1 X 8 DG DA DG DC DT DG DT DG CRYST1 134.363 134.363 47.695 90.00 90.00 120.00 P 63 6 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 0.007443 0.004297 0.000000 0.00000 SCALE2 0.000000 0.008594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020967 0.00000 MASTER 285 0 0 0 0 0 0 6 855 4 0 4 END