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- PDB-4u67: Crystal structure of the large ribosomal subunit (50S) of Deinoco... -

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Basic information

Entry
Database: PDB / ID: 4u67
TitleCrystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22
Components
  • (50S ribosomal protein ...) x 26
  • 23s RNA
  • 5s RNA5S ribosomal RNA
KeywordsRIBOSOME / Antibiotics / Resistance / Erythromycin
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Factor Xa Inhibitor - #60 / Ribosomal protein L25, C-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L6 ...Factor Xa Inhibitor - #60 / Ribosomal protein L25, C-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L6 / Ribosomal Protein L25; Chain P / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Factor Xa Inhibitor / Aldehyde Oxidoreductase; domain 3 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / RRM (RNA recognition motif) domain / Single Sheet / Nucleic acid-binding proteins / Ribosomal protein L16 signature 1. / : / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Beta Complex / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / 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 L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsWekselman, I. / Zimmerman, E. / Rozenberg, H. / Bashan, A. / Yonath, A.
CitationJournal: Structure / Year: 2017
Title: The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel.
Authors: Wekselman, I. / Zimmerman, E. / Davidovich, C. / Belousoff, M. / Matzov, D. / Krupkin, M. / Rozenberg, H. / Bashan, A. / Friedlander, G. / Kjeldgaard, J. / Ingmer, H. / Lindahl, L. / Zengel, J.M. / Yonath, A.
History
DepositionJul 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L2
B: 50S ribosomal protein L3
C: 50S ribosomal protein L4
D: 50S ribosomal protein L5
E: 50S ribosomal protein L6
G: 50S ribosomal protein L13
H: 50S ribosomal protein L14
I: 50S ribosomal protein L15
J: 50S ribosomal protein L16
K: 50S ribosomal protein L17
L: 50S ribosomal protein L18
M: 50S ribosomal protein L19
N: 50S ribosomal protein L20
O: 50S ribosomal protein L21
P: 50S ribosomal protein L22
Q: 50S ribosomal protein L23
R: 50S ribosomal protein L24
S: 50S ribosomal protein L25
T: 50S ribosomal protein L27
U: 50S ribosomal protein L28
V: 50S ribosomal protein L29
W: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
X: 23s RNA
Y: 5s RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,346,68979
Polymers1,345,44928
Non-polymers1,24051
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150110 Å2
ΔGint-1761 kcal/mol
Surface area457670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.720, 412.591, 696.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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50S ribosomal protein ... , 26 types, 26 molecules ABCDEGHIJKLMNOPQRSTUVWZ123

#1: Protein 50S ribosomal protein L2 /


Mass: 30107.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ9
#2: Protein 50S ribosomal protein L3 /


Mass: 22477.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXK2
#3: Protein 50S ribosomal protein L4 /


Mass: 22308.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXK1
#4: Protein 50S ribosomal protein L5 /


Mass: 20379.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ0
#5: Protein 50S ribosomal protein L6 /


Mass: 19613.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSL3
#6: Protein 50S ribosomal protein L13 /


Mass: 19223.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXY1
#7: Protein 50S ribosomal protein L14 /


Mass: 14256.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ2
#8: Protein 50S ribosomal protein L15 /


Mass: 16894.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSK9
#9: Protein 50S ribosomal protein L16 /


Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ5
#10: Protein 50S ribosomal protein L17 /


Mass: 12926.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSJ5
#11: Protein 50S ribosomal protein L18 /


Mass: 12163.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSL2
#12: Protein 50S ribosomal protein L19 /


Mass: 18347.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RWB4
#13: Protein 50S ribosomal protein L20 /


Mass: 13991.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSW7
#14: Protein 50S ribosomal protein L21 /


Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RY64
#15: Protein 50S ribosomal protein L22 /


Mass: 15544.310 Da / Num. of mol.: 1 / Mutation: Insertion of VPR after R109 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ7
#16: Protein 50S ribosomal protein L23 /


Mass: 10539.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXK0
#17: Protein 50S ribosomal protein L24 /


Mass: 12253.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ1
#18: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RX88
#19: Protein 50S ribosomal protein L27 /


Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RY65
#20: Protein 50S ribosomal protein L28 /


Mass: 8982.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RRG8
#21: Protein 50S ribosomal protein L29 /


Mass: 7774.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RXJ4
#22: Protein 50S ribosomal protein L30 /


Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSL0
#23: Protein 50S ribosomal protein L32 /


Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: P49228
#24: Protein 50S ribosomal protein L33 /


Mass: 6374.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSS4
#25: Protein/peptide 50S ribosomal protein L34 /


Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSH2
#26: Protein 50S ribosomal protein L35 /


Mass: 7448.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: UniProt: Q9RSW6

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RNA chain , 2 types, 2 molecules XY

#27: RNA chain 23s RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: GenBank: 11612676
#28: RNA chain 5s RNA / 5S ribosomal RNA


Mass: 39605.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
References: GenBank: 11612676

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Non-polymers , 1 types, 51 molecules

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


Mass: 24.305 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.53 Å3/Da / Density % sol: 72.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 261274 / % possible obs: 95.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 109.2 Å2 / Net I/σ(I): 7.3
Reflection shellResolution: 3.65→3.71 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.43 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJR

2zjr


Resolution: 3.65→19.991 Å / FOM work R set: 0.7759 / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2699 12927 5.03 %
Rwork0.2257 244165 -
obs0.228 257092 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 310.29 Å2 / Biso mean: 90.34 Å2 / Biso min: 25.03 Å2
Refinement stepCycle: final / Resolution: 3.65→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23862 59856 51 0 83769
Biso mean--40.99 --
Num. residues----5866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791262
X-RAY DIFFRACTIONf_angle_d1.192137070
X-RAY DIFFRACTIONf_chiral_restr0.06317539
X-RAY DIFFRACTIONf_plane_restr0.0067035
X-RAY DIFFRACTIONf_dihedral_angle_d17.25142864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.65-3.69120.36474120.32027786819892
3.6912-3.73440.33344330.31457724815793
3.7344-3.77960.35924280.30677870829893
3.7796-3.82710.36534100.30097966837694
3.8271-3.87710.33674170.29347975839295
3.8771-3.92980.28824070.28148069847695
3.9298-3.98560.32514190.27758050846996
3.9856-4.04460.31354340.27778125855996
4.0446-4.10720.33684310.27178068849996
4.1072-4.1740.31174210.27388201862297
4.174-4.24530.30894080.24998189859797
4.2453-4.32170.28134380.24578123856197
4.3217-4.4040.27634510.24178159861097
4.404-4.49290.28654470.23448187863497
4.4929-4.58940.28144600.23238156861697
4.5894-4.69480.28784350.22428187862297
4.6948-4.81070.26284360.2218181861797
4.8107-4.93880.24523970.2038254865197
4.9388-5.08180.24254410.20378210865197
5.0818-5.2430.22584470.19618232867997
5.243-5.42680.25344500.19628248869897
5.4268-5.63940.23854030.19338308871197
5.6394-5.88980.24384380.18818277871598
5.8898-6.19160.25864500.19648266871697
6.1916-6.56650.25714490.19498322877197
6.5665-7.05280.24444440.19158213865797
7.0528-7.72510.23354320.198274870696
7.7251-8.75960.25754420.20488209865196
8.7596-10.74330.24364170.20888231864895
10.7433-19.99160.25114300.22438105853592
Refinement TLS params.Method: refined / Origin x: 41.2151 Å / Origin y: 77.3983 Å / Origin z: 109.8839 Å
111213212223313233
T0.2175 Å2-0.1712 Å20.1079 Å2-0.9767 Å2-0.3083 Å2--0.2959 Å2
L0.4783 °20.0472 °20.0048 °2-0.1668 °20.123 °2--0.5484 °2
S-0.0109 Å °0.3759 Å °-0.1357 Å °-0.325 Å °0.0467 Å °-0.1105 Å °0.1436 Å °-0.1355 Å °-0.0047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 272
2X-RAY DIFFRACTION1allB1 - 205
3X-RAY DIFFRACTION1allC2 - 195
4X-RAY DIFFRACTION1allD3 - 179
5X-RAY DIFFRACTION1allE5 - 175
6X-RAY DIFFRACTION1allG30 - 171
7X-RAY DIFFRACTION1allH1 - 134
8X-RAY DIFFRACTION1allI11 - 144
9X-RAY DIFFRACTION1allJ6 - 141
10X-RAY DIFFRACTION1allK3 - 115
11X-RAY DIFFRACTION1allL8 - 111
12X-RAY DIFFRACTION1allM2 - 109
13X-RAY DIFFRACTION1allN2 - 118
14X-RAY DIFFRACTION1allO5 - 98
15X-RAY DIFFRACTION1allP8 - 137
16X-RAY DIFFRACTION1allQ2 - 94
17X-RAY DIFFRACTION1allR4 - 113
18X-RAY DIFFRACTION1allS1 - 175
19X-RAY DIFFRACTION1allT12 - 85
20X-RAY DIFFRACTION1allU8 - 79
21X-RAY DIFFRACTION1allV2 - 66
22X-RAY DIFFRACTION1allW1 - 55
23X-RAY DIFFRACTION1allZ4 - 59
24X-RAY DIFFRACTION1all12 - 54
25X-RAY DIFFRACTION1all21 - 46
26X-RAY DIFFRACTION1all36 - 64
27X-RAY DIFFRACTION1allX1 - 2877
28X-RAY DIFFRACTION1allY2 - 123
29X-RAY DIFFRACTION1allX2878 - 2881
30X-RAY DIFFRACTION1allK116
31X-RAY DIFFRACTION1allX2882 - 2918
32X-RAY DIFFRACTION1allP138
33X-RAY DIFFRACTION1allX2919 - 2926

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