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- PDB-3hkz: The X-ray crystal structure of RNA polymerase from Archaea -

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Basic information

Entry
Database: PDB / ID: 3hkz
TitleThe X-ray crystal structure of RNA polymerase from Archaea
Components
  • (DNA-directed RNA polymerase subunit ...) x 10
  • (DNA-directed RNA polymerase, subunit ...) x 3
KeywordsTRANSFERASE / RNA polymerase / archaea / Sulfolobus solfataricus / DNA-directed RNA polymerase / Metal-binding / Nucleotidyltransferase / Transcription / Zinc / Zinc-finger
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase I / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding ...3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase I / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
DNA Excision Repair, Uvrb; Chain A - #10 / DNA Excision Repair, Uvrb; Chain A / Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / RNA polymerase Rpo13 subunit HTH domain ...DNA Excision Repair, Uvrb; Chain A - #10 / DNA Excision Repair, Uvrb; Chain A / Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / Dihydrolipoamide Transferase / HRDC domain / RNA polymerase ii / RNA polymerase Rpb1 funnel domain / N-terminal domain of TfIIb / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Other non-globular / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, domain 2 / Helix Hairpins / Gyrase A; domain 2 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / Homeodomain-like / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / Helix non-globular / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo7 / RNA_pol_Rpo13 domain-containing protein / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase, subunit G (RpoG) / DNA-directed RNA polymerase subunit Rpo5 ...FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo7 / RNA_pol_Rpo13 domain-containing protein / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase, subunit G (RpoG) / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo4
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMurakami, K.S.
CitationJournal: Nature / Year: 2008
Title: The X-ray crystal structure of RNA polymerase from Archaea.
Authors: Hirata, A. / Klein, B.J. / Murakami, K.S.
History
DepositionMay 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 4, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _diffrn_source.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.0Sep 6, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit A'
C: DNA-directed RNA polymerase subunit A''
B: DNA-directed RNA polymerase subunit B
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase, subunit E' (RpoE1)
F: DNA-directed RNA polymerase, subunit F (RpoF)
G: DNA-directed RNA polymerase, subunit G (RpoG)
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
Y: DNA-directed RNA polymerase subunit 13
I: DNA-directed RNA polymerase subunit A'
M: DNA-directed RNA polymerase subunit A''
J: DNA-directed RNA polymerase subunit B
O: DNA-directed RNA polymerase subunit D
Q: DNA-directed RNA polymerase, subunit E' (RpoE1)
R: DNA-directed RNA polymerase, subunit F (RpoF)
S: DNA-directed RNA polymerase, subunit G (RpoG)
T: DNA-directed RNA polymerase subunit H
U: DNA-directed RNA polymerase subunit K
V: DNA-directed RNA polymerase subunit L
W: DNA-directed RNA polymerase subunit N
X: DNA-directed RNA polymerase subunit P
Z: DNA-directed RNA polymerase subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)811,62240
Polymers810,32826
Non-polymers1,29414
Water00
1
A: DNA-directed RNA polymerase subunit A'
C: DNA-directed RNA polymerase subunit A''
B: DNA-directed RNA polymerase subunit B
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase, subunit E' (RpoE1)
F: DNA-directed RNA polymerase, subunit F (RpoF)
G: DNA-directed RNA polymerase, subunit G (RpoG)
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
Y: DNA-directed RNA polymerase subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,81120
Polymers405,16413
Non-polymers6477
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: DNA-directed RNA polymerase subunit A'
M: DNA-directed RNA polymerase subunit A''
J: DNA-directed RNA polymerase subunit B
O: DNA-directed RNA polymerase subunit D
Q: DNA-directed RNA polymerase, subunit E' (RpoE1)
R: DNA-directed RNA polymerase, subunit F (RpoF)
S: DNA-directed RNA polymerase, subunit G (RpoG)
T: DNA-directed RNA polymerase subunit H
U: DNA-directed RNA polymerase subunit K
V: DNA-directed RNA polymerase subunit L
W: DNA-directed RNA polymerase subunit N
X: DNA-directed RNA polymerase subunit P
Z: DNA-directed RNA polymerase subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,81120
Polymers405,16413
Non-polymers6477
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.820, 201.235, 196.050
Angle α, β, γ (deg.)90.00, 100.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21I
12C
22M
13B
23J
14D
24O
15E
25Q
16F
26R
17G
27S
18H
28T
19K
29U
110L
210V
111N
211W
112P
212X
113Y
213Z

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYSAA4 - 8794 - 879
21LYSLYSLYSLYSIN4 - 8794 - 879
12PROPROARGARGCB11 - 39511 - 395
22PROPROARGARGMO11 - 39511 - 395
13LEULEUVALVALBC5 - 11195 - 1119
23LEULEUVALVALJP5 - 11195 - 1119
14SERSERLYSLYSDD2 - 2652 - 265
24SERSERLYSLYSOQ2 - 2652 - 265
15METMETLYSLYSEE1 - 1801 - 180
25METMETLYSLYSQR1 - 1801 - 180
16METMETMETMETFF1 - 891 - 89
26METMETMETMETRS1 - 891 - 89
17VALVALGLNGLNGG5 - 1175 - 117
27VALVALGLNGLNST5 - 1175 - 117
18ILEILEILEILEHH9 - 829 - 82
28ILEILEILEILETU9 - 829 - 82
19GLNGLNLEULEUKI11 - 9211 - 92
29GLNGLNLEULEUUV11 - 9211 - 92
110METMETLYSLYSLJ1 - 921 - 92
210METMETLYSLYSVW1 - 921 - 92
111METMETARGARGNK1 - 641 - 64
211METMETARGARGWX1 - 641 - 64
112CYSCYSILEILEPL6 - 486 - 48
212CYSCYSILEILEXY6 - 486 - 48
113ILEILEARGARGYM38 - 8238 - 82
213ILEILEARGARGZZ38 - 8238 - 82

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13

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Components

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DNA-directed RNA polymerase subunit ... , 10 types, 20 molecules AICMBJDOHTKULVNWPXYZ

#1: Protein DNA-directed RNA polymerase subunit A'


Mass: 99815.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980R2, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit A''


Mass: 43865.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: P58192, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit B


Mass: 126721.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980R1*PLUS
#4: Protein DNA-directed RNA polymerase subunit D


Mass: 30330.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: P95989, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit H


Mass: 9687.307 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980Q9, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit K


Mass: 10871.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q97ZJ9, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit L


Mass: 10298.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980K0, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase subunit N


Mass: 7602.009 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980Z8, DNA-directed RNA polymerase
#12: Protein/peptide DNA-directed RNA polymerase subunit P


Mass: 5606.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q97ZX7, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase subunit 13


Mass: 12198.671 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980B8

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DNA-directed RNA polymerase, subunit ... , 3 types, 6 molecules EQFRGS

#5: Protein DNA-directed RNA polymerase, subunit E' (RpoE1)


Mass: 20354.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980A3, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase, subunit F (RpoF) / Putative uncharacterized protein ORF-c20_042


Mass: 12825.573 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q9UXD9, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase, subunit G (RpoG)


Mass: 14985.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980L5, DNA-directed RNA polymerase

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Non-polymers , 3 types, 14 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.1 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5414 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. all: 105621 / Num. obs: 105621

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Processing

SoftwareName: REFMAC / Version: 5.5.0072 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9T

1r9t


Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.778 / SU B: 49.519 / SU ML: 0.792 / Cross valid method: THROUGHOUT / ESU R Free: 0.923 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34089 5323 5 %RANDOM
Rwork0.26542 ---
obs0.26922 100295 80.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-4.84 Å2
2--1.57 Å20 Å2
3----3.83 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53046 0 26 0 53072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02254012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.98272992
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.93356636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63523.752400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.3391510044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.86515448
X-RAY DIFFRACTIONr_chiral_restr0.1090.28328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02139986
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7431.533222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.418254006
X-RAY DIFFRACTIONr_scbond_it1.58320790
X-RAY DIFFRACTIONr_scangle_it3.0444.518980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
13344TIGHT POSITIONAL0.030.05
13329MEDIUM POSITIONAL0.040.5
13344TIGHT THERMAL0.050.5
13329MEDIUM THERMAL0.062
21480TIGHT POSITIONAL0.350.05
21388MEDIUM POSITIONAL0.590.5
21480TIGHT THERMAL0.350.5
21388MEDIUM THERMAL0.442
34360TIGHT POSITIONAL0.030.05
34285MEDIUM POSITIONAL0.040.5
34360TIGHT THERMAL0.050.5
34285MEDIUM THERMAL0.062
41056TIGHT POSITIONAL0.030.05
41058MEDIUM POSITIONAL0.030.5
41056TIGHT THERMAL0.040.5
41058MEDIUM THERMAL0.042
5704TIGHT POSITIONAL0.340.05
5698MEDIUM POSITIONAL0.580.5
5704TIGHT THERMAL0.240.5
5698MEDIUM THERMAL0.322
6356TIGHT POSITIONAL0.410.05
6339MEDIUM POSITIONAL0.70.5
6356TIGHT THERMAL0.180.5
6339MEDIUM THERMAL0.262
7452TIGHT POSITIONAL0.310.05
7433MEDIUM POSITIONAL0.530.5
7452TIGHT THERMAL0.290.5
7433MEDIUM THERMAL0.382
8296TIGHT POSITIONAL0.320.05
8316MEDIUM POSITIONAL0.560.5
8296TIGHT THERMAL0.270.5
8316MEDIUM THERMAL0.382
9328TIGHT POSITIONAL0.280.05
9331MEDIUM POSITIONAL0.540.5
9328TIGHT THERMAL0.340.5
9331MEDIUM THERMAL0.572
10368TIGHT POSITIONAL0.340.05
10355MEDIUM POSITIONAL0.480.5
10368TIGHT THERMAL0.440.5
10355MEDIUM THERMAL0.512
11256TIGHT POSITIONAL0.030.05
11258MEDIUM POSITIONAL0.030.5
11256TIGHT THERMAL0.040.5
11258MEDIUM THERMAL0.042
12172TIGHT POSITIONAL0.030.05
12174MEDIUM POSITIONAL0.030.5
12172TIGHT THERMAL0.040.5
12174MEDIUM THERMAL0.042
13180TIGHT POSITIONAL0.480.05
13212MEDIUM POSITIONAL0.770.5
13180TIGHT THERMAL0.190.5
13212MEDIUM THERMAL0.282
LS refinement shellResolution: 3.4→3.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 239 -
Rwork0.364 4969 -
obs--54 %

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