HEADER RNA 12-AUG-20 7JRS TITLE CRYSTAL STRUCTURES OF ARTIFICIALLY DESIGNED HOMOMERIC RNA TITLE 2 NANOARCHITECTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA 3D NANOCAGE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS NANO STRUCTURE, DIMERIC PARALLELOGRAM, RNA EXPDTA X-RAY DIFFRACTION AUTHOR D.LIU,Y.SHAO,J.A.PICCIRILLI,Y.WEIZMANN REVDAT 3 18-OCT-23 7JRS 1 REMARK REVDAT 2 06-OCT-21 7JRS 1 JRNL REVDAT 1 08-SEP-21 7JRS 0 JRNL AUTH D.LIU,Y.SHAO,J.A.PICCIRILLI,Y.WEIZMANN JRNL TITL STRUCTURES OF ARTIFICIALLY DESIGNED DISCRETE RNA JRNL TITL 2 NANOARCHITECTURES AT NEAR-ATOMIC RESOLUTION. JRNL REF SCI ADV V. 7 F4459 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 34550747 JRNL DOI 10.1126/SCIADV.ABF4459 REMARK 2 REMARK 2 RESOLUTION. 3.21 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) : 3.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15105 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.275 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1517 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 38.2890 - 7.1254 0.95 1193 135 0.2169 0.2153 REMARK 3 2 7.1254 - 5.6615 0.99 1245 140 0.2910 0.2918 REMARK 3 3 5.6615 - 4.9476 0.99 1247 137 0.2831 0.3322 REMARK 3 4 4.9476 - 4.4960 0.99 1265 142 0.3183 0.3350 REMARK 3 5 4.4960 - 4.1741 0.99 1236 141 0.3233 0.3677 REMARK 3 6 4.1741 - 3.9283 0.99 1246 140 0.2897 0.3304 REMARK 3 7 3.9283 - 3.7317 0.99 1250 141 0.2929 0.4068 REMARK 3 8 3.7317 - 3.5694 0.99 1217 136 0.3192 0.3280 REMARK 3 9 3.5694 - 3.4321 0.99 1242 139 0.3728 0.4639 REMARK 3 10 3.4321 - 3.3137 0.99 1246 135 0.3754 0.4306 REMARK 3 11 3.3137 - 3.2102 0.95 1201 131 0.3734 0.4338 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) : 0.550 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 151.8 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 : 0.001 6218 REMARK 3 ANGLE : 0.318 9702 REMARK 3 CHIRALITY : 0.017 1290 REMARK 3 PLANARITY : 0.001 258 REMARK 3 DIHEDRAL : 12.524 3090 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 7JRS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-16 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 : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 718 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 718 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15105 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.210 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.80400 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: PHENIX 1.11.1_2575 REMARK 200 STARTING MODEL: PDB ID: 4CS1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM MGCL2, 0.3 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 50 MM SODIUM SUCCINATE PH 5.5, 3.0 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP1 G A 40 O2' A B 64 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 7JRS A 1 129 PDB 7JRS 7JRS 1 129 DBREF 7JRS B 1 129 PDB 7JRS 7JRS 1 129 SEQRES 1 A 129 G G A C G C G G U A G C G SEQRES 2 A 129 A A G A A C C A U C G A C SEQRES 3 A 129 U G C G A C U U A G C G A SEQRES 4 A 129 G C C U G C C C U G G C A SEQRES 5 A 129 G U G G G A G C C U G A A SEQRES 6 A 129 G C A G G C A C G G G C G SEQRES 7 A 129 A A G A A C A C U G U C A SEQRES 8 A 129 G G U C G C U G A G U C G SEQRES 9 A 129 G C G U C C C A G U U G A SEQRES 10 A 129 U G G G G A G C U A C C SEQRES 1 B 129 G G A C G C G G U A G C G SEQRES 2 B 129 A A G A A C C A U C G A C SEQRES 3 B 129 U G C G A C U U A G C G A SEQRES 4 B 129 G C C U G C C C U G G C A SEQRES 5 B 129 G U G G G A G C C U G A A SEQRES 6 B 129 G C A G G C A C G G G C G SEQRES 7 B 129 A A G A A C A C U G U C A SEQRES 8 B 129 G G U C G C U G A G U C G SEQRES 9 B 129 G C G U C C C A G U U G A SEQRES 10 B 129 U G G G G A G C U A C C CRYST1 60.623 64.795 69.578 85.70 64.25 79.91 P 1 2 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 0.016495 -0.002936 -0.007962 0.00000 SCALE2 0.000000 0.015676 0.000021 0.00000 SCALE3 0.000000 0.000000 0.015957 0.00000