HEADER DNA 21-JUL-20 7JHR TITLE SELF-ASSEMBLY OF A 3D DNA CRYSTAL LATTICE (4X6 JUNCTION VERSION) TITLE 2 CONTAINING THE J4 IMMOBILE HOLLIDAY JUNCTION WITH R3 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*GP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*CP*GP*GP*GP*AP*CP*TP*CP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*TP*CP*TP*CP*CP*G)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*CP*GP*GP*TP*CP*TP*GP*C)- COMPND 15 3'); COMPND 16 CHAIN: D; COMPND 17 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 STRUCTURAL DNA NANOTECHNOLOGY, IMMOBILE HOLLIDAY JUNCTIONS, 3D DNA KEYWDS 2 SELF-ASSEMBLY, DESIGNER DNA CRYSTALS, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.R.SIMMONS,T.MACCULLOCH,N.STEPHANOPOULOS,H.YAN REVDAT 3 18-OCT-23 7JHR 1 REMARK REVDAT 2 06-JUL-22 7JHR 1 JRNL REVDAT 1 14-JUL-21 7JHR 0 JRNL AUTH C.R.SIMMONS,T.MACCULLOCH,M.KREPL,M.MATTHIES,A.BUCHBERGER, JRNL AUTH 2 I.CRAWFORD,J.SPONER,P.SULC,N.STEPHANOPOULOS,H.YAN JRNL TITL THE INFLUENCE OF HOLLIDAY JUNCTION SEQUENCE AND DYNAMICS ON JRNL TITL 2 DNA CRYSTAL SELF-ASSEMBLY. JRNL REF NAT COMMUN V. 13 3112 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35662248 JRNL DOI 10.1038/S41467-022-30779-6 REMARK 2 REMARK 2 RESOLUTION. 3.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.1 REMARK 3 NUMBER OF REFLECTIONS : 3279 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 330 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 43.7290 - 3.9782 1.00 1854 207 0.2297 0.2664 REMARK 3 2 3.9782 - 3.1580 0.59 1095 123 0.3417 0.3411 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 48.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 94.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 145.4 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 : 0.004 956 REMARK 3 ANGLE : 0.635 1467 REMARK 3 CHIRALITY : 0.031 166 REMARK 3 PLANARITY : 0.003 42 REMARK 3 DIHEDRAL : 35.401 406 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 7JHR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-19 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3297 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.4 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 26.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.30800 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: 6XNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 ML OF 0.05 M CACODYLATE PH 7.0 REMARK 280 WITH 20 MM MGCL2, 1.0 MM SPERMINE, 1.0 MM COH18N6, AND 15% REMARK 280 ETHANOL WAS ADDED TO THE RESERVOIR WITH 2 UL ADDED TO THE DROP REMARK 280 CONTAINING 4 UL OF DNA STOCK, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 57.57500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.24094 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.21900 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.57500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.24094 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.21900 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.57500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.24094 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.21900 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.48188 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 32.43800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.48188 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 32.43800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.48188 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 32.43800 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CAC C 101 REMARK 610 CAC D 101 DBREF 7JHR A 1 12 PDB 7JHR 7JHR 1 12 DBREF 7JHR B 12 20 PDB 7JHR 7JHR 12 20 DBREF 7JHR C 0 5 PDB 7JHR 7JHR 0 5 DBREF 7JHR D 2 16 PDB 7JHR 7JHR 2 16 SEQRES 1 A 12 DG DA DG DC DA DG DA DC DC DA DG DA SEQRES 1 B 9 DC DG DG DG DA DC DT DC DA SEQRES 1 C 6 DT DC DT DC DC DG SEQRES 1 D 15 DT DC DT DG DA DG DT DC DG DG DT DC DT SEQRES 2 D 15 DG DC HET CAC C 101 1 HET CAC D 101 1 HETNAM CAC CACODYLATE ION HETSYN CAC DIMETHYLARSINATE FORMUL 5 CAC 2(C2 H6 AS O2 1-) CRYST1 115.150 115.150 48.657 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 0.008684 0.005014 0.000000 0.00000 SCALE2 0.000000 0.010028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020552 0.00000