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- PDB-2c37: RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA -

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Basic information

Entry
Database: PDB / ID: 2c37
TitleRNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA
Components(PROBABLE EXOSOME COMPLEX EXONUCLEASE ...) x 2
KeywordsHYDROLASE / EXOSOME / RRP41 / RRP42 / EXORIBONUCLEASE / RNA DEGRADATION / ARCHAEAL
Function / homology
Function and homology information


cytoplasmic exosome (RNase complex) / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / gene expression / RNA binding
Similarity search - Function
Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / GHMP Kinase, N-terminal domain / : / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily ...Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / GHMP Kinase, N-terminal domain / : / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-O-phosphono-beta-D-ribofuranose / URIDINE-5'-MONOPHOSPHATE / Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLorentzen, E. / Conti, E.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core.
Authors: Lorentzen, E. / Conti, E.
History
DepositionOct 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_database_status / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
C: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
D: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
E: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
F: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
G: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
H: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
I: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
J: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
K: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
L: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
M: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
N: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
O: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
P: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
Q: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
R: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
S: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
T: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
U: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
V: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
W: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
X: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)702,87063
Polymers694,08724
Non-polymers8,78339
Water00
1
A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
C: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
D: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
E: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
F: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,22117
Polymers173,5226
Non-polymers2,70011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
H: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
I: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
J: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
K: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
L: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,57315
Polymers173,5226
Non-polymers2,0519
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
M: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
N: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
O: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
P: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
Q: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
R: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,83113
Polymers173,5226
Non-polymers1,3097
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
S: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
T: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
U: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
V: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
W: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
X: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,24418
Polymers173,5226
Non-polymers2,72312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)207.020, 212.940, 433.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
91Q
101S
111U
121W
12B
22D
32F
42H
52J
62L
72N
82P
92R
102T
112V
122X
13D
23L
33P
43R
53T

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPROAA1 - 741 - 74
211METMETPROPROCC1 - 741 - 74
311METMETPROPROEE1 - 741 - 74
411METMETPROPROGG1 - 741 - 74
511METMETPROPROII1 - 741 - 74
611METMETPROPROKK1 - 741 - 74
711METMETPROPROMM1 - 741 - 74
811METMETPROPROOO1 - 741 - 74
911METMETPROPROQQ1 - 741 - 74
1011METMETPROPROSS1 - 741 - 74
1111METMETPROPROUU1 - 741 - 74
1211METMETPROPROWW1 - 741 - 74
121GLUGLUSERSERAA76 - 12176 - 121
221GLUGLUSERSERCC76 - 12176 - 121
321GLUGLUSERSEREE76 - 12176 - 121
421GLUGLUSERSERGG76 - 12176 - 121
521GLUGLUSERSERII76 - 12176 - 121
621GLUGLUSERSERKK76 - 12176 - 121
721GLUGLUSERSERMM76 - 12176 - 121
821GLUGLUSERSEROO76 - 12176 - 121
921GLUGLUSERSERQQ76 - 12176 - 121
1021GLUGLUSERSERSS76 - 12176 - 121
1121GLUGLUSERSERUU76 - 12176 - 121
1221GLUGLUSERSERWW76 - 12176 - 121
131ALAALAPROPROAA123 - 231123 - 231
231ALAALAPROPROCC123 - 231123 - 231
331ALAALAPROPROEE123 - 231123 - 231
431ALAALAPROPROGG123 - 231123 - 231
531ALAALAPROPROII123 - 231123 - 231
631ALAALAPROPROKK123 - 231123 - 231
731ALAALAPROPROMM123 - 231123 - 231
831ALAALAPROPROOO123 - 231123 - 231
931ALAALAPROPROQQ123 - 231123 - 231
1031ALAALAPROPROSS123 - 231123 - 231
1131ALAALAPROPROUU123 - 231123 - 231
1231ALAALAPROPROWW123 - 231123 - 231
141LEULEUILEILEAA233 - 275233 - 275
241LEULEUILEILECC233 - 275233 - 275
341LEULEUILEILEEE233 - 275233 - 275
441LEULEUILEILEGG233 - 275233 - 275
541LEULEUILEILEII233 - 275233 - 275
641LEULEUILEILEKK233 - 275233 - 275
741LEULEUILEILEMM233 - 275233 - 275
841LEULEUILEILEOO233 - 275233 - 275
941LEULEUILEILEQQ233 - 275233 - 275
1041LEULEUILEILESS233 - 275233 - 275
1141LEULEUILEILEUU233 - 275233 - 275
1241LEULEUILEILEWW233 - 275233 - 275
112LYSLYSASPASPBB18 - 18218 - 182
212LYSLYSASPASPDD18 - 18218 - 182
312LYSLYSASPASPFF18 - 18218 - 182
412LYSLYSASPASPHH18 - 18218 - 182
512LYSLYSASPASPJJ18 - 18218 - 182
612LYSLYSASPASPLL18 - 18218 - 182
712LYSLYSASPASPNN18 - 18218 - 182
812LYSLYSASPASPPP18 - 18218 - 182
912LYSLYSASPASPRR18 - 18218 - 182
1012LYSLYSASPASPTT18 - 18218 - 182
1112LYSLYSASPASPVV18 - 18218 - 182
1212LYSLYSASPASPXX18 - 18218 - 182
122TRPTRPVALVALBB184 - 248184 - 248
222TRPTRPVALVALDD184 - 248184 - 248
322TRPTRPVALVALFF184 - 248184 - 248
422TRPTRPVALVALHH184 - 248184 - 248
522TRPTRPVALVALJJ184 - 248184 - 248
622TRPTRPVALVALLL184 - 248184 - 248
722TRPTRPVALVALNN184 - 248184 - 248
822TRPTRPVALVALPP184 - 248184 - 248
922TRPTRPVALVALRR184 - 248184 - 248
1022TRPTRPVALVALTT184 - 248184 - 248
1122TRPTRPVALVALVV184 - 248184 - 248
1222TRPTRPVALVALXX184 - 248184 - 248
113GLUGLULYSLYSDD8 - 188 - 18
213GLUGLULYSLYSLL8 - 188 - 18
313GLUGLULYSLYSPP8 - 188 - 18
413GLUGLULYSLYSRR8 - 188 - 18
513GLUGLULYSLYSTT8 - 188 - 18

NCS ensembles :
ID
1
2
3

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Components

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PROBABLE EXOSOME COMPLEX EXONUCLEASE ... , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2


Mass: 30227.625 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC0, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1


Mass: 27612.936 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE / 5-O-phosphono-beta-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 38 molecules

#3: Chemical...
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growpH: 7 / Details: 50 MM MES, 2.4 M SODIUM MALONATE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.951
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 211093 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.7 / % possible all: 83.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR2

2br2


Resolution: 2.8→93.25 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.862 / SU B: 39.895 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R: 1.031 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 6530 3 %RANDOM
Rwork0.266 ---
obs0.267 211093 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46133 0 437 0 46570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02247224
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1972.00764091
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03455996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44324.9211839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47158470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31215287
X-RAY DIFFRACTIONr_chiral_restr0.0760.27713
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0234335
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.220487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.231853
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.21611
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.2198
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3621.530135
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72248606
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.079317458
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9654.515485
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1897tight positional0.030.05
12C1897tight positional0.040.05
13E1897tight positional0.030.05
14G1897tight positional0.030.05
15I1897tight positional0.030.05
16K1897tight positional0.040.05
17M1897tight positional0.030.05
18O1897tight positional0.040.05
19Q1897tight positional0.040.05
110S1897tight positional0.040.05
111U1897tight positional0.040.05
112W1897tight positional0.040.05
21B1753tight positional0.030.05
22D1753tight positional0.040.05
23F1753tight positional0.040.05
24H1753tight positional0.030.05
25J1753tight positional0.030.05
26L1753tight positional0.040.05
27N1753tight positional0.040.05
28P1753tight positional0.040.05
29R1753tight positional0.040.05
210T1753tight positional0.040.05
211V1753tight positional0.030.05
212X1753tight positional0.030.05
31D69tight positional0.040.05
32L69tight positional0.040.05
33P69tight positional0.060.05
34R69tight positional0.040.05
35T69tight positional0.040.05
11A1897tight thermal0.050.5
12C1897tight thermal0.060.5
13E1897tight thermal0.050.5
14G1897tight thermal0.050.5
15I1897tight thermal0.050.5
16K1897tight thermal0.060.5
17M1897tight thermal0.060.5
18O1897tight thermal0.060.5
19Q1897tight thermal0.060.5
110S1897tight thermal0.060.5
111U1897tight thermal0.060.5
112W1897tight thermal0.060.5
21B1753tight thermal0.060.5
22D1753tight thermal0.060.5
23F1753tight thermal0.060.5
24H1753tight thermal0.060.5
25J1753tight thermal0.060.5
26L1753tight thermal0.060.5
27N1753tight thermal0.060.5
28P1753tight thermal0.060.5
29R1753tight thermal0.070.5
210T1753tight thermal0.060.5
211V1753tight thermal0.060.5
212X1753tight thermal0.060.5
31D69tight thermal0.060.5
32L69tight thermal0.050.5
33P69tight thermal0.070.5
34R69tight thermal0.050.5
35T69tight thermal0.050.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 426
Rwork0.357 13746

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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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