HEADER RNA 24-JUL-24 9CSO TITLE 16MER SELF-COMPLEMENTARY DUPLEX RNA WITH S(2)C:G PAIR SEQUENCE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA STRAND WITH S(2)C:G PAIR SEQUENCE 1; 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 2-THIOCYTIDINE, NUCLEOBASE MODIFICATION, NON-CANONICAL BASE PAIR, KEYWDS 2 RNA, ORGIN OF LIFE EXPDTA X-RAY DIFFRACTION AUTHOR Z.FANG,X.JIA,J.W.SZOSTAK REVDAT 2 28-MAY-25 9CSO 1 JRNL REVDAT 1 14-MAY-25 9CSO 0 JRNL AUTH Z.FANG,X.JIA,Y.XING,J.W.SZOSTAK JRNL TITL NONENZYMATIC RNA COPYING WITH A POTENTIALLY PRIMORDIAL JRNL TITL 2 GENETIC ALPHABET. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 20122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40397670 JRNL DOI 10.1073/PNAS.2505720122 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 8258 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 429 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2517 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2085 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.2707 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 336 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.33 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9CSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000285478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-24 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000026 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.50400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 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 (%): 38.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 20.66950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 11.93354 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.38200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 20.66950 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 11.93354 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.38200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 20.66950 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 11.93354 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.38200 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 20.66950 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 11.93354 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.38200 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 20.66950 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 11.93354 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 41.38200 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 20.66950 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 11.93354 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 41.38200 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 23.86708 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 82.76400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 23.86708 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 82.76400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 23.86708 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 82.76400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 23.86708 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 82.76400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 23.86708 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 82.76400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 23.86708 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 82.76400 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: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 109 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 133 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 144 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 151 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 152 LIES ON A SPECIAL POSITION. 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 O HOH A 124 O HOH A 177 2.10 REMARK 500 O2 U A 11 O HOH A 101 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 104 O HOH A 173 2545 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G A 7 O5' G A 7 C5' -0.059 REMARK 500 U A 11 C2 U A 11 N3 -0.080 REMARK 500 REMARK 500 REMARK: NULL 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 A A 1 C6 - N1 - C2 ANGL. DEV. = 4.3 DEGREES REMARK 500 A A 1 N1 - C2 - N3 ANGL. DEV. = -4.4 DEGREES REMARK 500 G A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 6 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 6 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 A A 6 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 G A 7 O5' - P - OP1 ANGL. DEV. = -6.8 DEGREES REMARK 500 A A 8 C2 - N3 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 C A 10 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 C A 13 O5' - P - OP2 ANGL. DEV. = -7.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9CSO A 1 16 PDB 9CSO 9CSO 1 16 SEQRES 1 A 16 A G A G A A G A U C U U C SEQRES 2 A 16 U RSP U HET RSP A 15 20 HETNAM RSP 4-AMINO-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL) HETNAM 2 RSP PYRIMIDINE-2(1H)-THIONE FORMUL 1 RSP C9 H14 N3 O7 P S FORMUL 2 HOH *88(H2 O) LINK O3' U A 14 P RSP A 15 1555 1555 1.57 LINK O3' RSP A 15 P U A 16 1555 1555 1.57 CRYST1 41.339 41.339 124.146 90.00 90.00 120.00 H 3 2 18 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 0.024190 0.013966 0.000000 0.00000 SCALE2 0.000000 0.027932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008055 0.00000 HETATM 297 P RSP A 15 6.059 -22.628 21.405 1.00 11.33 P HETATM 298 N1 RSP A 15 10.246 -20.910 18.953 1.00 6.52 N HETATM 299 C2 RSP A 15 11.114 -20.019 18.281 1.00 9.30 C HETATM 300 S2 RSP A 15 12.589 -20.478 17.865 1.00 9.37 S HETATM 301 N3 RSP A 15 10.618 -18.718 18.071 1.00 7.70 N HETATM 302 C4 RSP A 15 9.327 -18.412 18.442 1.00 8.16 C HETATM 303 N4 RSP A 15 8.900 -17.136 18.118 1.00 8.09 N HETATM 304 C5 RSP A 15 8.428 -19.294 19.116 1.00 7.82 C HETATM 305 C6 RSP A 15 8.948 -20.567 19.389 1.00 7.72 C HETATM 306 C1' RSP A 15 10.716 -22.283 19.076 1.00 9.09 C HETATM 307 C2' RSP A 15 11.619 -22.507 20.269 1.00 9.01 C HETATM 308 O2' RSP A 15 12.441 -23.630 19.972 1.00 11.11 O HETATM 309 C3' RSP A 15 10.592 -22.849 21.313 1.00 9.31 C HETATM 310 O3' RSP A 15 11.162 -23.498 22.423 1.00 9.78 O HETATM 311 C4' RSP A 15 9.669 -23.760 20.532 1.00 9.31 C HETATM 312 O4' RSP A 15 9.581 -23.120 19.253 1.00 10.28 O HETATM 313 C5' RSP A 15 8.283 -23.958 21.104 1.00 11.55 C HETATM 314 O5' RSP A 15 7.619 -22.704 21.163 1.00 9.98 O HETATM 315 OP1 RSP A 15 5.666 -23.551 22.495 1.00 14.69 O HETATM 316 OP2 RSP A 15 5.774 -21.183 21.530 1.00 14.58 O TER 337 U A 16 HETATM 338 O HOH A 101 -0.169 -15.631 6.651 1.00 27.17 O HETATM 339 O HOH A 102 14.434 -15.237 -1.615 1.00 34.52 O HETATM 340 O HOH A 103 3.603 -6.242 0.000 0.50 23.31 O HETATM 341 O HOH A 104 19.732 -20.853 -4.175 1.00 28.90 O HETATM 342 O HOH A 105 10.623 -20.556 -7.262 1.00 32.26 O HETATM 343 O HOH A 106 -0.489 -20.416 21.602 1.00 22.69 O HETATM 344 O HOH A 107 -3.324 -14.686 17.309 1.00 30.34 O HETATM 345 O HOH A 108 -0.163 -18.316 -10.243 1.00 20.44 O HETATM 346 O HOH A 109 20.670 -11.934 -2.792 0.33 17.87 O HETATM 347 O HOH A 110 5.832 -14.729 15.778 1.00 21.44 O HETATM 348 O HOH A 111 19.246 -15.196 2.410 1.00 24.97 O HETATM 349 O HOH A 112 -0.229 -19.774 -18.203 1.00 24.64 O HETATM 350 O HOH A 113 9.521 -12.433 2.513 1.00 25.71 O HETATM 351 O HOH A 114 3.282 -17.758 19.638 1.00 28.51 O HETATM 352 O HOH A 115 8.891 -15.964 -10.795 1.00 20.76 O HETATM 353 O HOH A 116 6.798 -13.822 10.475 1.00 28.20 O HETATM 354 O HOH A 117 15.273 -18.856 -1.252 1.00 37.57 O HETATM 355 O HOH A 118 2.755 -11.326 11.057 1.00 28.82 O HETATM 356 O HOH A 119 7.251 -16.569 21.898 1.00 19.68 O HETATM 357 O HOH A 120 4.788 -14.998 -14.748 1.00 28.70 O HETATM 358 O HOH A 121 5.457 -18.712 20.703 1.00 23.56 O HETATM 359 O HOH A 122 6.516 -16.473 -11.761 1.00 12.40 O HETATM 360 O HOH A 123 15.613 -9.282 5.770 1.00 31.82 O HETATM 361 O HOH A 124 10.740 -18.254 -7.369 1.00 25.66 O HETATM 362 O HOH A 125 8.820 -14.391 -3.691 1.00 27.09 O HETATM 363 O HOH A 126 2.026 -19.699 -19.172 1.00 20.96 O HETATM 364 O HOH A 127 9.391 -24.935 -5.789 1.00 25.31 O HETATM 365 O HOH A 128 2.378 -24.487 -10.479 1.00 32.23 O HETATM 366 O HOH A 129 7.927 -23.123 24.729 1.00 24.29 O HETATM 367 O HOH A 130 -2.159 -20.952 11.565 1.00 23.48 O HETATM 368 O HOH A 131 13.523 -25.749 23.817 1.00 20.48 O HETATM 369 O HOH A 132 16.110 -17.638 26.057 1.00 14.38 O HETATM 370 O HOH A 133 0.001 -23.866 16.588 0.33 12.52 O HETATM 371 O HOH A 134 8.764 -26.445 -12.495 1.00 19.60 O HETATM 372 O HOH A 135 16.537 -15.284 20.625 1.00 27.00 O HETATM 373 O HOH A 136 6.086 -12.120 -18.960 1.00 30.18 O HETATM 374 O HOH A 137 16.486 -24.630 -9.061 1.00 27.02 O HETATM 375 O HOH A 138 4.131 -17.183 -11.877 1.00 23.33 O HETATM 376 O HOH A 139 10.963 -22.861 -14.895 1.00 11.41 O HETATM 377 O HOH A 140 8.784 -27.049 -9.208 1.00 28.08 O HETATM 378 O HOH A 141 8.513 -19.373 -9.756 1.00 22.86 O HETATM 379 O HOH A 142 5.254 -23.254 -16.550 1.00 14.30 O HETATM 380 O HOH A 143 7.334 -11.627 8.694 1.00 46.13 O HETATM 381 O HOH A 144 20.669 -11.934 -6.276 0.33 14.13 O HETATM 382 O HOH A 145 -2.731 -12.271 15.252 1.00 31.83 O HETATM 383 O HOH A 146 18.446 -14.778 -8.923 1.00 27.81 O HETATM 384 O HOH A 147 11.408 -14.825 -2.587 1.00 27.82 O HETATM 385 O HOH A 148 1.643 -13.994 13.830 1.00 20.58 O HETATM 386 O HOH A 149 12.115 -11.931 0.767 1.00 30.10 O HETATM 387 O HOH A 150 9.382 -7.475 6.373 1.00 28.43 O HETATM 388 O HOH A 151 20.669 -11.934 -0.145 0.33 19.81 O HETATM 389 O HOH A 152 0.000 -23.867 19.568 0.33 15.16 O HETATM 390 O HOH A 153 -0.703 -9.328 4.494 1.00 24.02 O HETATM 391 O HOH A 154 9.030 -10.975 5.840 1.00 27.34 O HETATM 392 O HOH A 155 12.942 -19.436 -5.308 1.00 27.38 O HETATM 393 O HOH A 156 16.929 -6.350 4.588 1.00 31.08 O HETATM 394 O HOH A 157 8.340 -20.077 23.122 1.00 19.31 O HETATM 395 O HOH A 158 5.852 -26.468 19.291 1.00 14.76 O HETATM 396 O HOH A 159 9.390 -13.477 -0.479 1.00 27.25 O HETATM 397 O HOH A 160 17.677 -6.310 0.075 1.00 20.47 O HETATM 398 O HOH A 161 11.695 -9.443 3.854 1.00 20.68 O HETATM 399 O HOH A 162 8.641 -2.288 0.527 1.00 32.89 O HETATM 400 O HOH A 163 7.685 -14.087 -16.363 1.00 16.52 O HETATM 401 O HOH A 164 2.222 -16.771 16.747 1.00 22.76 O HETATM 402 O HOH A 165 10.119 -20.391 26.588 1.00 26.36 O HETATM 403 O HOH A 166 15.756 -20.347 -14.291 1.00 24.64 O HETATM 404 O HOH A 167 6.205 -18.130 -9.840 1.00 21.80 O HETATM 405 O HOH A 168 2.127 -18.206 -8.935 1.00 25.35 O HETATM 406 O HOH A 169 6.097 -25.747 -7.807 1.00 29.75 O HETATM 407 O HOH A 170 13.524 -7.981 6.862 1.00 33.22 O HETATM 408 O HOH A 171 1.112 -21.466 9.711 1.00 31.18 O HETATM 409 O HOH A 172 6.151 -16.568 19.087 1.00 16.91 O HETATM 410 O HOH A 173 12.191 -4.968 -3.578 1.00 28.42 O HETATM 411 O HOH A 174 16.489 -21.198 -1.094 1.00 32.86 O HETATM 412 O HOH A 175 4.732 -13.980 13.268 1.00 21.87 O HETATM 413 O HOH A 176 13.085 -20.006 26.648 1.00 26.09 O HETATM 414 O HOH A 177 9.360 -16.892 -8.175 1.00 30.04 O HETATM 415 O HOH A 178 12.885 -25.216 -13.732 1.00 27.31 O HETATM 416 O HOH A 179 9.541 -24.757 26.730 1.00 35.32 O HETATM 417 O HOH A 180 18.952 -10.890 -7.328 1.00 26.86 O HETATM 418 O HOH A 181 18.573 -11.919 3.329 1.00 31.55 O HETATM 419 O HOH A 182 5.408 -4.508 -0.877 1.00 32.28 O HETATM 420 O HOH A 183 12.643 -14.498 -0.026 1.00 30.82 O HETATM 421 O HOH A 184 1.751 -22.926 22.457 1.00 29.80 O HETATM 422 O HOH A 185 11.037 -11.736 4.681 1.00 41.36 O HETATM 423 O HOH A 186 12.508 -10.920 6.229 1.00 29.22 O HETATM 424 O HOH A 187 2.246 -18.731 -6.705 1.00 31.08 O HETATM 425 O HOH A 188 2.602 -15.695 -8.497 1.00 31.88 O CONECT 285 297 CONECT 297 285 314 315 316 CONECT 298 299 305 306 CONECT 299 298 300 301 CONECT 300 299 CONECT 301 299 302 CONECT 302 301 303 304 CONECT 303 302 CONECT 304 302 305 CONECT 305 298 304 CONECT 306 298 307 312 CONECT 307 306 308 309 CONECT 308 307 CONECT 309 307 310 311 CONECT 310 309 317 CONECT 311 309 312 313 CONECT 312 306 311 CONECT 313 311 314 CONECT 314 297 313 CONECT 315 297 CONECT 316 297 CONECT 317 310 MASTER 389 0 1 0 0 0 0 6 424 1 22 2 END