HEADER RNA 16-JUN-23 8PFK TITLE RNA STRUCTURE WITH 1-METHYLPSEUDORIDINE, C2 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (12-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SARS-COV-2, COVID-19, CORONAVIRUS, MRNA VACCINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.SPINGLER,K.MCAULEY,P.NIEVERGELT,A.THORN REVDAT 3 01-MAY-24 8PFK 1 JRNL REVDAT 2 24-APR-24 8PFK 1 JRNL REVDAT 1 31-JAN-24 8PFK 0 JRNL AUTH P.NIEVERGELT,F.BERLIAT,K.E.MCAULEY,C.R.DORGAN,R.M.VAN WELL, JRNL AUTH 2 A.THORN,B.SPINGLER JRNL TITL RNA OLIGOMERS AT ATOMIC RESOLUTION CONTAINING JRNL TITL 2 1-METHYLPSEUDOURIDINE, AN ESSENTIAL BUILDING BLOCK OF MRNA JRNL TITL 3 VACCINES. JRNL REF CHEMMEDCHEM V. 19 00600 2024 JRNL REFN ESSN 1860-7187 JRNL PMID 38235959 JRNL DOI 10.1002/CMDC.202300600 REMARK 2 REMARK 2 RESOLUTION. 1.32 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 7504 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 376 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 23.7500 - 1.9000 1.00 2694 142 0.1376 0.1840 REMARK 3 2 1.9000 - 1.5100 1.00 2632 139 0.1590 0.1598 REMARK 3 3 1.5100 - 1.3210 0.68 1802 95 0.1719 0.2493 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) : 0.093 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.767 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.29 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 : 0.006 286 REMARK 3 ANGLE : 0.950 445 REMARK 3 CHIRALITY : 0.034 58 REMARK 3 PLANARITY : 0.011 12 REMARK 3 DIHEDRAL : 6.566 134 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 8PFK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14352 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.321 REMARK 200 RESOLUTION RANGE LOW (A) : 23.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.01578 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 37.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33540 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.110 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 (%): 46.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 % V/V MPD, 40 MM SODIUM CACODYLATE, REMARK 280 12 MM SPERMINE, 80 MM SODIUM CHLORIDE, 12 MM POTASSIUM CHLORIDE REMARK 280 AND 20 MM MAGNESIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 20.64750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.38850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.64750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.38850 REMARK 290 SMTRY3 4 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 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 221 O HOH A 250 3556 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 211 O REMARK 620 2 HOH A 227 O 89.8 REMARK 620 3 HOH A 242 O 85.4 91.9 REMARK 620 4 HOH A 282 O 90.3 85.0 174.8 REMARK 620 5 HOH A 289 O 176.3 93.5 96.1 88.3 REMARK 620 6 HOH A 295 O 84.6 174.4 87.3 95.3 92.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 235 O REMARK 620 2 HOH A 243 O 89.1 REMARK 620 3 HOH A 254 O 86.7 69.1 REMARK 620 4 HOH A 269 O 84.0 172.6 107.5 REMARK 620 5 HOH A 283 O 87.5 90.3 158.6 92.3 REMARK 620 6 HOH A 291 O 175.5 88.6 96.2 98.4 88.5 REMARK 620 N 1 2 3 4 5 DBREF 8PFK A 1 12 PDB 8PFK 8PFK 1 12 SEQRES 1 A 12 C G C G A A B8H U A G C G HET B8H A 7 33 HET MG A 101 1 HET MG A 102 1 HETNAM B8H [(2~{R},3~{S},4~{R},5~{S})-5-[1-METHYL-2,4- HETNAM 2 B8H BIS(OXIDANYLIDENE)PYRIMIDIN-5-YL]-3,4-BIS(OXIDANYL) HETNAM 3 B8H OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 B8H C10 H15 N2 O9 P FORMUL 2 MG 2(MG 2+) FORMUL 4 HOH *95(H2 O) LINK O3' A A 6 P B8H A 7 1555 1555 1.60 LINK O3' B8H A 7 P U A 8 1555 1555 1.61 LINK MG MG A 101 O HOH A 211 1555 1555 2.22 LINK MG MG A 101 O HOH A 227 1555 1555 2.11 LINK MG MG A 101 O HOH A 242 1555 1555 1.93 LINK MG MG A 101 O HOH A 282 1555 1555 2.23 LINK MG MG A 101 O HOH A 289 1555 1555 2.12 LINK MG MG A 101 O HOH A 295 1555 1555 2.08 LINK MG MG A 102 O HOH A 235 1555 1555 2.06 LINK MG MG A 102 O HOH A 243 1555 1555 2.04 LINK MG MG A 102 O HOH A 254 1555 1555 2.77 LINK MG MG A 102 O HOH A 269 1555 2555 2.08 LINK MG MG A 102 O HOH A 283 1555 1555 2.20 LINK MG MG A 102 O HOH A 291 1555 2555 2.05 CRYST1 41.295 34.777 31.685 90.00 128.07 90.00 C 1 2 1 4 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 0.024216 0.000000 0.018967 0.00000 SCALE2 0.000000 0.028755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040089 0.00000