HEADER DNA 12-JAN-26 10CH TITLE [011SE] TWO TURN TENSEGRITY TRIANGLE WITH 0,1 AND 1 BP STICKY ENDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*GP*AP*TP*GP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*AP*TP*AP*AP*A)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*AP*TP*CP*G)-3'); COMPND 9 CHAIN: E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*TP*TP*TP*AP*TP*GP*TP*GP*GP*TP*CP*GP*CP*T)-3'); COMPND 13 CHAIN: D; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'- COMPND 17 D(*GP*AP*GP*CP*GP*AP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)- COMPND 18 3'); COMPND 19 CHAIN: B; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*GP*T)-3'); COMPND 23 CHAIN: F; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 6; COMPND 26 MOLECULE: DNA (5'- COMPND 27 D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)- COMPND 28 3'); COMPND 29 CHAIN: C; COMPND 30 ENGINEERED: YES; COMPND 31 MOL_ID: 7; COMPND 32 MOLECULE: DNA (5'- COMPND 33 D(*AP*CP*AP*CP*CP*GP*AP*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*T)- COMPND 34 3'); COMPND 35 CHAIN: M; COMPND 36 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; SOURCE 17 MOL_ID: 5; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630; SOURCE 21 MOL_ID: 6; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 MOL_ID: 7; SOURCE 26 SYNTHETIC: YES; SOURCE 27 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 28 ORGANISM_TAXID: 32630 KEYWDS TENSEGRITY TRIANGLE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.VECCHIONI,K.WOLOSZYN,R.SHA,Y.P.OHAYON REVDAT 1 25-MAR-26 10CH 0 JRNL AUTH S.VECCHIONI,K.WOLOSZYN,R.SHA,Y.P.OHAYON,L.PERREN JRNL TITL SHAPE ANISOTROPY IN 3D DNA ARCHITECTURES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.45 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) : 4.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 61.9 REMARK 3 NUMBER OF REFLECTIONS : 4579 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.600 REMARK 3 FREE R VALUE TEST SET COUNT : 302 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 40.9300 - 5.6000 0.96 3289 255 0.2076 0.2186 REMARK 3 2 5.6000 - 4.4500 0.28 988 47 0.3079 0.3977 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) : 0.737 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 46.225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 214.6 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 203.3 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 : 0.007 2873 REMARK 3 ANGLE : 0.995 4421 REMARK 3 CHIRALITY : 0.052 498 REMARK 3 PLANARITY : 0.005 126 REMARK 3 DIHEDRAL : 42.118 1233 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 10CH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1000304169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.000000 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 : 4589 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.446 REMARK 200 RESOLUTION RANGE LOW (A) : 51.927 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 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): 8.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MOPS, 1.25 M MAGNESIUM SULFATE, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: HEPTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEPTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, D, B, F, C, M 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 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 102 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 103 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG A 106 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC A 107 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 111 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC A 117 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA E 103 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA E 103 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG E 104 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT E 105 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DT E 105 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG E 110 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 102 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 104 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA D 105 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 107 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 111 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT F 103 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA F 105 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA F 105 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG F 110 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT M 121 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 10CH A 102 122 PDB 10CH 10CH 102 122 DBREF 10CH E 102 115 PDB 10CH 10CH 102 115 DBREF 10CH D 102 115 PDB 10CH 10CH 102 115 DBREF 10CH B 101 121 PDB 10CH 10CH 101 121 DBREF 10CH F 102 115 PDB 10CH 10CH 102 115 DBREF 10CH C 101 121 PDB 10CH 10CH 101 121 DBREF 10CH M 101 121 PDB 10CH 10CH 101 121 SEQRES 1 A 21 DC DG DA DT DG DC DC DT DG DA DT DC DG SEQRES 2 A 21 DG DA DC DA DT DA DA DA SEQRES 1 E 14 DT DA DG DT DC DG DT DG DG DC DA DT DC SEQRES 2 E 14 DG SEQRES 1 D 14 DT DT DT DA DT DG DT DG DG DT DC DG DC SEQRES 2 D 14 DT SEQRES 1 B 21 DG DA DG DC DG DA DC DC DT DG DT DA DC SEQRES 2 B 21 DG DG DA DC DA DT DC DA SEQRES 1 F 14 DC DT DG DA DT DG DT DG DG DT DA DG DG SEQRES 2 F 14 DT SEQRES 1 C 21 DA DA DC DC DT DA DC DC DT DG DG DC DA SEQRES 2 C 21 DG DG DA DC DG DA DC DT SEQRES 1 M 21 DA DC DA DC DC DG DA DT DC DA DC DC DT SEQRES 2 M 21 DG DC DC DA DC DC DG DT CRYST1 67.618 68.133 69.809 96.73 98.46 99.85 P 1 1 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 0.014789 0.002568 0.002603 0.00000 SCALE2 0.000000 0.014897 0.002200 0.00000 SCALE3 0.000000 0.000000 0.014639 0.00000 MASTER 221 0 0 0 0 0 0 6 2565 7 0 14 END