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- PDB-5dfe: 70S termination complex containing E. coli RF2 -

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Basic information

Entry
Database: PDB / ID: 5dfe
Title70S termination complex containing E. coli RF2
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S rRNA
  • 5S rRNA
  • P-site tRNA fMet
  • Peptide chain release factor 2
  • T23S rRNA
  • messenger RNA
KeywordsRIBOSOME / PROTEIN BIOSYNTHESIS / RIBOSOMES / RNA / tRNA / TRANSFER RNA / 30S / 50S / 70S / 16S / 23S / RIBOSOMAL SUBUNIT / RF2 / RELEASE FACTOR 2 / PEPTIDE CHAIN TERMINATION / RELEASE FACTOR / BACTERIAL PROTEINS / CODON / MOLECULAR PEPTIDE CHAIN TERMINATION / TRANSLATIONAL
Function / homology
Function and homology information


translation release factor activity, codon specific / translational termination / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly ...translation release factor activity, codon specific / translational termination / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / viral translational frameshifting / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein L20
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...IRON/SULFUR CLUSTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Peptide chain release factor RF2 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus HB8 (bacteria)
Thermus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09997551079 Å
AuthorsHoffer, E.D. / Dunham, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093278 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112641 United States
CitationJournal: Cell Rep / Year: 2016
Title: Uniformity of Peptide Release Is Maintained by Methylation of Release Factors.
Authors: Pierson, W.E. / Hoffer, E.D. / Keedy, H.E. / Simms, C.L. / Dunham, C.M. / Zaher, H.S.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Structure summary
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
QV: P-site tRNA fMet
QX: messenger RNA
QY: Peptide chain release factor 2
XV: P-site tRNA fMet
XX: messenger RNA
XY: Peptide chain release factor 2
YA: T23S rRNA
YB: 5S rRNA
YD: 50S ribosomal protein L2
YE: 50S ribosomal protein L3
YF: 50S ribosomal protein L4
YG: 50S ribosomal protein L5
YH: 50S ribosomal protein L6
YI: 50S ribosomal protein L9
YN: 50S ribosomal protein L13
YO: 50S ribosomal protein L14
YP: 50S ribosomal protein L15
YQ: 50S ribosomal protein L16
YR: 50S ribosomal protein L17
YS: 50S ribosomal protein L18
YT: 50S ribosomal protein L19
YU: 50S ribosomal protein L20
YV: 50S ribosomal protein L21
YW: 50S ribosomal protein L22
YX: 50S ribosomal protein L23
YY: 50S ribosomal protein L24
YZ: 50S ribosomal protein L25
Y0: 50S ribosomal protein L27
Y1: 50S ribosomal protein L28
Y2: 50S ribosomal protein L29
Y3: 50S ribosomal protein L30
Y4: 50S ribosomal protein L31
Y5: 50S ribosomal protein L32
Y6: 50S ribosomal protein L33
Y7: 50S ribosomal protein L34
Y8: 50S ribosomal protein L35
Y9: 50S ribosomal protein L36
XA: 16S rRNA
XB: 30S ribosomal protein S2
XC: 30S ribosomal protein S3
XD: 30S ribosomal protein S4
XE: 30S ribosomal protein S5
XF: 30S ribosomal protein S6
XG: 30S ribosomal protein S7
XH: 30S ribosomal protein S8
XI: 30S ribosomal protein S9
XJ: 30S ribosomal protein S10
XK: 30S ribosomal protein S11
XL: 30S ribosomal protein S12
XM: 30S ribosomal protein S13
XN: 30S ribosomal protein S14 type Z
XO: 30S ribosomal protein S15
XP: 30S ribosomal protein S16
XQ: 30S ribosomal protein S17
XR: 30S ribosomal protein S18
XS: 30S ribosomal protein S19
XT: 30S ribosomal protein S20
XU: 30S ribosomal protein Thx
QA: 16S rRNA
QB: 30S ribosomal protein S2
QC: 30S ribosomal protein S3
QD: 30S ribosomal protein S4
QE: 30S ribosomal protein S5
QF: 30S ribosomal protein S6
QG: 30S ribosomal protein S7
QH: 30S ribosomal protein S8
QI: 30S ribosomal protein S9
QJ: 30S ribosomal protein S10
QK: 30S ribosomal protein S11
QL: 30S ribosomal protein S12
QM: 30S ribosomal protein S13
QN: 30S ribosomal protein S14 type Z
QO: 30S ribosomal protein S15
QP: 30S ribosomal protein S16
QQ: 30S ribosomal protein S17
QR: 30S ribosomal protein S18
QS: 30S ribosomal protein S19
QT: 30S ribosomal protein S20
QU: 30S ribosomal protein Thx
RA: T23S rRNA
RB: 5S rRNA
RD: 50S ribosomal protein L2
RE: 50S ribosomal protein L3
RF: 50S ribosomal protein L4
RG: 50S ribosomal protein L5
RH: 50S ribosomal protein L6
RI: 50S ribosomal protein L9
RN: 50S ribosomal protein L13
RO: 50S ribosomal protein L14
RP: 50S ribosomal protein L15
RQ: 50S ribosomal protein L16
RR: 50S ribosomal protein L17
RS: 50S ribosomal protein L18
RT: 50S ribosomal protein L19
RU: 50S ribosomal protein L20
RV: 50S ribosomal protein L21
RW: 50S ribosomal protein L22
RX: 50S ribosomal protein L23
RY: 50S ribosomal protein L24
RZ: 50S ribosomal protein L25
R0: 50S ribosomal protein L27
R1: 50S ribosomal protein L28
R2: 50S ribosomal protein L29
R3: 50S ribosomal protein L30
R4: 50S ribosomal protein L31
R5: 50S ribosomal protein L32
R6: 50S ribosomal protein L33
R7: 50S ribosomal protein L34
R8: 50S ribosomal protein L35
R9: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,552,1482637
Polymers4,489,582110
Non-polymers62,5672527
Water00
1
QV: P-site tRNA fMet
QX: messenger RNA
QY: Peptide chain release factor 2
QA: 16S rRNA
QB: 30S ribosomal protein S2
QC: 30S ribosomal protein S3
QD: 30S ribosomal protein S4
QE: 30S ribosomal protein S5
QF: 30S ribosomal protein S6
QG: 30S ribosomal protein S7
QH: 30S ribosomal protein S8
QI: 30S ribosomal protein S9
QJ: 30S ribosomal protein S10
QK: 30S ribosomal protein S11
QL: 30S ribosomal protein S12
QM: 30S ribosomal protein S13
QN: 30S ribosomal protein S14 type Z
QO: 30S ribosomal protein S15
QP: 30S ribosomal protein S16
QQ: 30S ribosomal protein S17
QR: 30S ribosomal protein S18
QS: 30S ribosomal protein S19
QT: 30S ribosomal protein S20
QU: 30S ribosomal protein Thx
RA: T23S rRNA
RB: 5S rRNA
RD: 50S ribosomal protein L2
RE: 50S ribosomal protein L3
RF: 50S ribosomal protein L4
RG: 50S ribosomal protein L5
RH: 50S ribosomal protein L6
RI: 50S ribosomal protein L9
RN: 50S ribosomal protein L13
RO: 50S ribosomal protein L14
RP: 50S ribosomal protein L15
RQ: 50S ribosomal protein L16
RR: 50S ribosomal protein L17
RS: 50S ribosomal protein L18
RT: 50S ribosomal protein L19
RU: 50S ribosomal protein L20
RV: 50S ribosomal protein L21
RW: 50S ribosomal protein L22
RX: 50S ribosomal protein L23
RY: 50S ribosomal protein L24
RZ: 50S ribosomal protein L25
R0: 50S ribosomal protein L27
R1: 50S ribosomal protein L28
R2: 50S ribosomal protein L29
R3: 50S ribosomal protein L30
R4: 50S ribosomal protein L31
R5: 50S ribosomal protein L32
R6: 50S ribosomal protein L33
R7: 50S ribosomal protein L34
R8: 50S ribosomal protein L35
R9: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,281,7011550
Polymers2,244,79155
Non-polymers36,9101495
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
XV: P-site tRNA fMet
XX: messenger RNA
XY: Peptide chain release factor 2
YA: T23S rRNA
YB: 5S rRNA
YD: 50S ribosomal protein L2
YE: 50S ribosomal protein L3
YF: 50S ribosomal protein L4
YG: 50S ribosomal protein L5
YH: 50S ribosomal protein L6
YI: 50S ribosomal protein L9
YN: 50S ribosomal protein L13
YO: 50S ribosomal protein L14
YP: 50S ribosomal protein L15
YQ: 50S ribosomal protein L16
YR: 50S ribosomal protein L17
YS: 50S ribosomal protein L18
YT: 50S ribosomal protein L19
YU: 50S ribosomal protein L20
YV: 50S ribosomal protein L21
YW: 50S ribosomal protein L22
YX: 50S ribosomal protein L23
YY: 50S ribosomal protein L24
YZ: 50S ribosomal protein L25
Y0: 50S ribosomal protein L27
Y1: 50S ribosomal protein L28
Y2: 50S ribosomal protein L29
Y3: 50S ribosomal protein L30
Y4: 50S ribosomal protein L31
Y5: 50S ribosomal protein L32
Y6: 50S ribosomal protein L33
Y7: 50S ribosomal protein L34
Y8: 50S ribosomal protein L35
Y9: 50S ribosomal protein L36
XA: 16S rRNA
XB: 30S ribosomal protein S2
XC: 30S ribosomal protein S3
XD: 30S ribosomal protein S4
XE: 30S ribosomal protein S5
XF: 30S ribosomal protein S6
XG: 30S ribosomal protein S7
XH: 30S ribosomal protein S8
XI: 30S ribosomal protein S9
XJ: 30S ribosomal protein S10
XK: 30S ribosomal protein S11
XL: 30S ribosomal protein S12
XM: 30S ribosomal protein S13
XN: 30S ribosomal protein S14 type Z
XO: 30S ribosomal protein S15
XP: 30S ribosomal protein S16
XQ: 30S ribosomal protein S17
XR: 30S ribosomal protein S18
XS: 30S ribosomal protein S19
XT: 30S ribosomal protein S20
XU: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,270,4481087
Polymers2,244,79155
Non-polymers25,6571032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.480, 450.410, 622.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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RNA chain , 5 types, 10 molecules QVXVQXXXYARAYBRBXAQA

#1: RNA chain P-site tRNA fMet


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1016582139
#2: RNA chain messenger RNA


Mass: 8196.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) synthetic construct (others)
#4: RNA chain T23S rRNA


Mass: 948035.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#5: RNA chain 5S rRNA


Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#35: RNA chain 16S rRNA


Mass: 493864.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382

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Protein , 1 types, 2 molecules QYXY

#3: Protein Peptide chain release factor 2 / RF-2


Mass: 42991.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: prfB, supK, b2891, JW5847 / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P07012

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50S ribosomal protein ... , 29 types, 58 molecules YDRDYEREYFRFYGRGYHRHYIRIYNRNYOROYPRPYQRQYRRRYSRSYTRTYURUYVRV...

#6: Protein 50S ribosomal protein L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#7: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#8: Protein 50S ribosomal protein L4 / L1e


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#9: Protein 50S ribosomal protein L5


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#10: Protein 50S ribosomal protein L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#11: Protein 50S ribosomal protein L9


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ1
#12: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#13: Protein 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP8
#14: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#15: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#16: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#17: Protein 50S ribosomal protein L18 / TL24


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#18: Protein 50S ribosomal protein L19


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#19: Protein 50S ribosomal protein L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#20: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#21: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#22: Protein 50S ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#23: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#24: Protein 50S ribosomal protein L25 / TL5


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#25: Protein 50S ribosomal protein L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#26: Protein 50S ribosomal protein L28


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60494
#27: Protein 50S ribosomal protein L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#28: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#29: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#30: Protein 50S ribosomal protein L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#31: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#32: Protein/peptide 50S ribosomal protein L34


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#33: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1
#34: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2

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30S ribosomal protein ... , 20 types, 40 molecules XBQBXCQCXDQDXEQEXFQFXGQGXHQHXIQIXJQJXKQKXLQLXMQMXNQNXOQOXPQP...

#36: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#37: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#38: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#39: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#40: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#41: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#42: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#43: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#44: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#45: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#46: Protein 30S ribosomal protein S12


Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#47: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#48: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#49: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#50: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#51: Protein 30S ribosomal protein S17


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#52: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#53: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#54: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#55: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

-
Non-polymers , 3 types, 2527 molecules

#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2513 / Source method: obtained synthetically / Formula: Mg
#57: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#58: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)
13.2962.6
23.2962.6
Crystal grow
Temperature (K)Crystal-IDMethodpHDetailsPH range
2931vapor diffusion, sitting drop75.5% PEG 20k, 11% PEG 200, 100 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8 mM DOBC7
2932vapor diffusion, sitting drop75.8% PEG 20k, 11.6% PEG 200, 200 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8mM DOBC7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2015
RadiationMonochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.09997551079→49.9 Å / Num. obs: 1057161 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 65.1513074296 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.269 / Net I/av σ(I): 8.98 / Net I/σ(I): 8.98
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.1-3.181.0021.820.577199.9
3.18-3.270.8422.260.664199.9
3.27-3.360.8793.040.749199.9
3.36-3.470.8163.560.7851100
3.47-3.580.7014.630.8641100
3.58-3.710.6285.020.8731100
3.71-3.850.5196.50.9261100
3.85-40.4516.980.9251100
4-4.180.388.370.9511100
4.18-4.380.32310.250.9691100
4.38-4.620.28311.570.9751100
4.62-4.90.25412.640.9781100
4.9-5.240.22213.790.9811100
5.24-5.660.20114.610.9831100
5.66-6.20.18516.120.9871100
6.2-6.930.16716.940.9881100
6.93-80.14518.610.989199.9
8-9.80.12121.740.9941100
9.8-13.860.09525.690.9961100
13.860.06127.760.995197.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155phasing
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y4O
Resolution: 3.09997551079→49.8846320819 Å / SU ML: 0.35301417503 / Cross valid method: FREE R-VALUE / σ(F): 1.36291542291 / Phase error: 20.0734461834
RfactorNum. reflection% reflectionSelection details
Rfree0.227251785283 49510 4.6835372389 %Inherited
Rwork0.195631996396 ---
obs0.197081129841 1057107 99.9591504427 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 77.0700635802 Å2
Refinement stepCycle: LAST / Resolution: 3.09997551079→49.8846320819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms97165 196956 2541 0 296662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047503827355319336
X-RAY DIFFRACTIONf_angle_d0.916861275819477071
X-RAY DIFFRACTIONf_chiral_restr0.046492015764260339
X-RAY DIFFRACTIONf_plane_restr0.0076491035441926374
X-RAY DIFFRACTIONf_dihedral_angle_d14.0328978407194217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.32905904012317070.29551506638133206X-RAY DIFFRACTION99.8341482943
3.1352-3.17210.30455516125917630.27414101007933261X-RAY DIFFRACTION99.9714562996
3.1721-3.21080.29934352238117290.26305977514133301X-RAY DIFFRACTION99.9743143355
3.2108-3.25140.28172172513917230.25355638502433313X-RAY DIFFRACTION99.9686135761
3.2514-3.29420.28047251340117720.24761481214933260X-RAY DIFFRACTION99.7835251225
3.2942-3.33930.27601105785417390.24029535466833308X-RAY DIFFRACTION99.9629207074
3.3393-3.3870.27397844079317500.23878510907233344X-RAY DIFFRACTION99.9829059829
3.387-3.43750.27127041469316920.2309814914533312X-RAY DIFFRACTION100
3.4375-3.49120.26133792373317520.22720503809533346X-RAY DIFFRACTION99.9943019943
3.4912-3.54840.26082190978917630.2217403978633246X-RAY DIFFRACTION100
3.5484-3.60960.24982207705617460.21153053606533395X-RAY DIFFRACTION100
3.6096-3.67520.23983391441116740.2107405482833422X-RAY DIFFRACTION99.9914527479
3.6752-3.74590.24444255820917520.20215541401933397X-RAY DIFFRACTION99.9971550498
3.7459-3.82230.22422621000417530.1941516549133399X-RAY DIFFRACTION99.9488200171
3.8223-3.90540.2239196700616870.19160237949133380X-RAY DIFFRACTION99.9429988315
3.9054-3.99620.22365866266417460.18722443140533393X-RAY DIFFRACTION99.9886179324
3.9962-4.09610.21129047997217570.18396866233366X-RAY DIFFRACTION99.9772280892
4.0961-4.20680.20344609259617430.17735308356133504X-RAY DIFFRACTION99.9801440971
4.2068-4.33050.19871928655417730.17629639091933373X-RAY DIFFRACTION99.9886201991
4.3305-4.47020.20461673908815070.1727688682633787X-RAY DIFFRACTION99.9915006941
4.4702-4.62990.1987708770649700.16912696034734199X-RAY DIFFRACTION99.9943134969
4.6299-4.81510.19911411795812020.17072263167334056X-RAY DIFFRACTION100
4.8151-5.03410.19414953208316000.16739514037733716X-RAY DIFFRACTION99.9858441154
5.0341-5.29920.19548948546517390.16256212373133573X-RAY DIFFRACTION99.9773499434
5.2992-5.63080.196093403217320.15989581259633599X-RAY DIFFRACTION99.9801912955
5.6308-6.06480.19909091001917540.1655295632533724X-RAY DIFFRACTION99.985908745
6.0648-6.67390.20470539282517510.17342209135233706X-RAY DIFFRACTION99.9718047763
6.6739-7.63670.20690185821412710.17849747761634348X-RAY DIFFRACTION99.9270584935
7.6367-9.61010.226587914213200.19697472119934491X-RAY DIFFRACTION99.9330263709
9.6101-49.89110.22821082911916430.21487190757434872X-RAY DIFFRACTION99.7568571741

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