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- PDB-5nrg: The crystal structure of the large ribosomal subunit of Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 5nrg
TitleThe crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with RB02
Components
  • (50S ribosomal protein ...) x 24
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / RNA / antibiotics / lincosamides
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, C-terminal domain / 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 L25; Chain P / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 ...Ribosomal protein L25, C-terminal domain / 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 L25; Chain P / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal protein L22/L17 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Aldehyde Oxidoreductase; domain 3 / RNA Polymerase Alpha Subunit; Chain A, 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 / Nucleic acid-binding proteins / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Beta Complex / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Few Secondary Structures / Irregular / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein L2, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L15, conserved site
Similarity search - Domain/homology
Chem-95H / : / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 ...Chem-95H / : / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.442 Å
AuthorsYonath, A. / Matzov, D. / Eyal, Z. / Ben Hamou, R. / Zimmerman, E. / Rozenberg, H. / Bashan, A. / Fridman, M.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.
Authors: Matzov, D. / Eyal, Z. / Benhamou, R.I. / Shalev-Benami, M. / Halfon, Y. / Krupkin, M. / Zimmerman, E. / Rozenberg, H. / Bashan, A. / Fridman, M. / Yonath, A.
History
DepositionApr 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 23S ribosomal RNA
Y: 5S ribosomal RNA
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
V: 50S ribosomal protein L29
W: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,344,441325
Polymers1,329,84026
Non-polymers14,601299
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area119790 Å2
ΔGint-1157 kcal/mol
Surface area462390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.797, 279.797, 873.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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RNA chain , 2 types, 2 molecules XY

#1: RNA chain 23S ribosomal RNA


Mass: 946687.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381
#2: RNA chain 5S ribosomal RNA


Mass: 36692.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381

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50S ribosomal protein ... , 24 types, 24 molecules ABCDEGHIJKLMNOPQRSTVWZ23

#3: Protein 50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P60430
#4: Protein 50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW06
#5: Protein 50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW07
#6: Protein 50S ribosomal protein L5


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW18
#7: Protein 50S ribosomal protein L6


Mass: 19818.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW21
#8: Protein 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW38
#9: Protein 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW16
#10: Protein 50S ribosomal protein L15


Mass: 15021.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P0A0F8
#11: Protein 50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW13
#12: Protein 50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW33
#13: Protein 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW22
#14: Protein 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FZ42
#15: Protein 50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: A7X3A1, UniProt: Q2FXQ1*PLUS
#16: Protein 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXS8
#17: Protein 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW11
#18: Protein 50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW08
#19: Protein 50S ribosomal protein L24


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW17
#20: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G0S0
#21: Protein 50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXT0
#22: Protein 50S ribosomal protein L29


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW14
#23: Protein 50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P0A0G2
#24: Protein 50S ribosomal protein L32


Mass: 6657.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FZF1
#25: Protein/peptide 50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FUQ0
#26: Protein 50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: A7X3A2, UniProt: Q2FXQ0*PLUS

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Non-polymers , 6 types, 299 molecules

#27: Chemical ChemComp-95H / ~{N}-[(1~{R},2~{R})-1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-methylsulfanyl-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanyl-propy l]-4-nitro-benzamide / RB02


Mass: 402.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N2O8S
#28: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#29: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 210 / Source method: obtained synthetically / Formula: Mn
#30: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 84 / Source method: obtained synthetically / Formula: Mg
#31: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#32: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 1:2 MPD: EtOH, Hepes pH=7.6 10mM, Mg2Cl 10mM, KCl 60mM, NH4Cl 15mM
PH range: 7.0-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.971 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 3.442→50 Å / Num. obs: 254888 / % possible obs: 96.3 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.052 / Rrim(I) all: 0.196 / Χ2: 1.072 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.45-3.513.60.7720.640.3750.8680.98972.8
3.51-3.574.60.7080.7130.3120.7820.98286.5
3.57-3.646.80.7520.7660.2730.8061.00694
3.64-3.728.40.6810.8290.2220.721.1597.5
3.72-3.89.20.6260.8920.1930.6591.03298.3
3.8-3.8910.30.5920.8840.170.6181.1399.1
3.89-3.9811.70.5270.9170.140.5481.14498.7
3.98-4.0912.30.4560.9380.1170.4731.09698.7
4.09-4.21130.4190.9530.1040.4341.10198.7
4.21-4.35130.3570.9620.0890.371.08498.4
4.35-4.512.80.3160.9650.080.3271.03798.5
4.5-4.6812.30.2620.9720.0690.2721.06498.8
4.68-4.8912.10.2310.9770.0620.241.07698.8
4.89-5.1513.40.2020.980.0510.211.06398.6
5.15-5.4713.40.1790.9830.0460.1851.07598.4
5.47-5.913.30.1650.9850.0430.1711.09498.3
5.9-6.4912.30.1510.9870.0410.1571.08198.2
6.49-7.4313.60.1340.9870.0350.1391.04298.3
7.43-9.3512.70.1190.990.0320.1241.01897.8
9.35-5012.40.1030.9940.0280.1071.04496.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WCE

4wce


Resolution: 3.442→49.369 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.78
RfactorNum. reflection% reflection
Rfree0.2613 12715 5 %
Rwork0.2189 --
obs0.221 254546 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 325.9 Å2 / Biso min: 25.81 Å2
Refinement stepCycle: final / Resolution: 3.442→49.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19867 60549 361 0 80777
Biso mean--84.61 --
Num. residues----5696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00987991
X-RAY DIFFRACTIONf_angle_d1.39133068
X-RAY DIFFRACTIONf_chiral_restr0.05817378
X-RAY DIFFRACTIONf_plane_restr0.0096432
X-RAY DIFFRACTIONf_dihedral_angle_d18.38740862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4421-3.48120.34662860.32615411569766
3.4812-3.52210.35153610.31286638699980
3.5221-3.56510.3283810.31027272765388
3.5651-3.61020.334110.30217682809393
3.6102-3.65770.3194060.2997982838897
3.6577-3.70770.31594180.2858112853098
3.7077-3.76070.3044410.28678131857298
3.7607-3.81680.29984350.28228219865499
3.8168-3.87640.31164370.2718204864199
3.8764-3.940.27823990.26518248864799
3.94-4.00790.27564440.25738173861799
4.0079-4.08070.28694340.25288180861499
4.0807-4.15920.2814440.24768224866899
4.1592-4.2440.2814400.24348206864699
4.244-4.33620.24794490.22888146859598
4.3362-4.4370.27184180.22958260867898
4.437-4.54790.26633970.22288230862799
4.5479-4.67080.26824400.22088309874999
4.6708-4.80810.2764380.21778238867699
4.8081-4.96320.27264390.21078243868299
4.9632-5.14040.24354650.20188223868899
5.1404-5.3460.22084280.19758264869298
5.346-5.5890.24274720.19358257872998
5.589-5.88320.23564110.19598324873598
5.8832-6.25110.23374410.19578298873998
6.2511-6.73270.26564490.19398349879898
6.7327-7.40820.2274210.18048390881198
7.4082-8.47550.24324610.17978412887398
8.4755-10.66050.23414300.17438455888597
10.6605-49.37370.23334190.19188751917095

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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