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- PDB-5d4c: Crystal structure of Thermus thermophilus product complex for tra... -

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Basic information

Entry
Database: PDB / ID: 5d4c
TitleCrystal structure of Thermus thermophilus product complex for transcription initiation with ATP and CTP
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • DNA (27-MER)
  • DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3')
  • RNA polymerase sigma factor SigA
Keywordstranscription/dna / RNA polymerase / transcription initiation / bacterial / NCIN / non-canonical initiating nucleotide / primer-dependent initiation / DNA / Single-Stranded / DNA-Directed RNA Polymerases / Gene Expression Regulation / Promoter Regions / Genetic / Protein Conformation / Sigma Factor / Thermus thermophilus / TRANSCRIPTION / transcription-dna complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / 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 / RNA polymerase subunit, RPB6/omega ...Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / 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 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / RNA polymerase Rpb6 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-MONOPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsZhang, Y. / Ebright, R.H.
CitationJournal: Nature / Year: 2016
Title: The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
Authors: Bird, J.G. / Zhang, Y. / Tian, Y. / Panova, N. / Barvik, I. / Greene, L. / Liu, M. / Buckley, B. / Krasny, L. / Lee, J.K. / Kaplan, C.D. / Ebright, R.H. / Nickels, B.E.
History
DepositionAug 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Aug 3, 2016Group: Database references
Revision 1.4Oct 12, 2016Group: Source and taxonomy
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / 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_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_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_type.id
Revision 2.0Jul 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.value_order / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.twist / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_comp_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 alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor SigA
G: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3')
H: DNA (27-MER)
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
P: RNA polymerase sigma factor SigA
R: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3')
S: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)889,38837
Polymers886,23216
Non-polymers3,15621
Water1,04558
1
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor SigA
G: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3')
H: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,68218
Polymers443,1168
Non-polymers1,56610
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52710 Å2
ΔGint-247 kcal/mol
Surface area143040 Å2
MethodPISA
2
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
P: RNA polymerase sigma factor SigA
R: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3')
S: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,70619
Polymers443,1168
Non-polymers1,59011
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52110 Å2
ΔGint-255 kcal/mol
Surface area142750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.960, 103.640, 297.420
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABKLCMDNEO

#1: Protein
DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 125436.539 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: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 170997.391 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: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11533.316 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: Q8RQE7, DNA-directed RNA polymerase

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Protein , 1 types, 2 molecules FP

#5: Protein RNA polymerase sigma factor SigA


Mass: 50769.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: sigA, TTHA0532 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1

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DNA chain , 2 types, 4 molecules GRHS

#6: DNA chain DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3')


Mass: 5845.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#7: DNA chain DNA (27-MER)


Mass: 8421.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

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Non-polymers , 6 types, 79 molecules

#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#11: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#12: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.76 % / Description: rod
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 100 mM Tris-HCl, pH 8.4, 200 mM potassium chloride, 50 mM magnesium chloride, 9.5% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 892176 / Num. obs: 164255 / % possible obs: 96.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 57.72 Å2 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.084 / Rrim(I) all: 0.197 / Rsym value: 0.185 / Χ2: 1.112 / Net I/av σ(I): 8.672 / Net I/σ(I): 5.6 / Num. measured all: 892176
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.3-3.3650.9541.66774750.7760.4410.97187.5
3.36-3.425.20.89175590.7930.4060.98689.80.983
3.42-3.485.30.74577140.8490.3361.00390.50.82
3.48-3.555.40.68177680.8830.3081.01791.60.75
3.55-3.635.40.55678290.8970.251.01592.20.612
3.63-3.725.40.46379320.9250.211.04792.90.51
3.72-3.815.40.40179470.9440.1811.05593.40.441
3.81-3.915.40.34480100.9570.1551.10194.80.379
3.91-4.035.40.28881540.970.131.13495.60.317
4.03-4.165.40.24182480.9760.1091.1696.60.265
4.16-4.315.40.21183310.9810.0951.16697.90.233
4.31-4.485.40.1883890.9850.0821.21598.70.198
4.48-4.685.40.16885030.9850.0761.24499.50.186
4.68-4.935.50.15485630.9890.071.19799.90.17
4.93-5.245.60.15385280.9880.071.18299.90.169
5.24-5.645.70.15685570.9870.0711.1811000.172
5.64-6.215.70.15285910.9890.0691.181000.167
6.21-7.15.60.13886050.9880.0631.2041000.152
7.1-8.945.50.09786650.9930.0461.1321000.107
8.94-505.50.07188870.9940.0340.9699.90.079

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H7H

4h7h


Resolution: 3.28→49.196 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 7724 5.01 %Random selection
Rwork0.2115 ---
obs0.2138 154105 89.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.28→49.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55006 1401 135 58 56600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457707
X-RAY DIFFRACTIONf_angle_d0.8178356
X-RAY DIFFRACTIONf_dihedral_angle_d14.04622384
X-RAY DIFFRACTIONf_chiral_restr0.0598817
X-RAY DIFFRACTIONf_plane_restr0.00410021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2803-3.31760.3436210.2898503X-RAY DIFFRACTION9
3.3176-3.35660.3908930.29181457X-RAY DIFFRACTION27
3.3566-3.39750.34571390.29722846X-RAY DIFFRACTION53
3.3975-3.44050.30272240.28754156X-RAY DIFFRACTION76
3.4405-3.48580.33372630.29524842X-RAY DIFFRACTION90
3.4858-3.53350.33212590.28284926X-RAY DIFFRACTION92
3.5335-3.5840.32292720.26625061X-RAY DIFFRACTION92
3.584-3.63740.31592550.25694890X-RAY DIFFRACTION92
3.6374-3.69430.29642750.25085105X-RAY DIFFRACTION93
3.6943-3.75480.29412630.23855044X-RAY DIFFRACTION93
3.7548-3.81950.26672670.24435144X-RAY DIFFRACTION94
3.8195-3.8890.2512680.23315095X-RAY DIFFRACTION94
3.889-3.96370.292770.22765180X-RAY DIFFRACTION95
3.9637-4.04460.2372720.22165206X-RAY DIFFRACTION96
4.0446-4.13250.25182820.21335284X-RAY DIFFRACTION97
4.1325-4.22860.23142770.21455270X-RAY DIFFRACTION97
4.2286-4.33430.27542820.20635391X-RAY DIFFRACTION99
4.3343-4.45140.25872840.19965342X-RAY DIFFRACTION99
4.4514-4.58230.22912850.19125409X-RAY DIFFRACTION99
4.5823-4.73010.22892860.1935477X-RAY DIFFRACTION100
4.7301-4.8990.23732870.18965447X-RAY DIFFRACTION100
4.899-5.09490.24772850.19315406X-RAY DIFFRACTION100
5.0949-5.32660.23212870.19115469X-RAY DIFFRACTION100
5.3266-5.6070.25192870.19265472X-RAY DIFFRACTION100
5.607-5.95780.26192860.19815453X-RAY DIFFRACTION100
5.9578-6.41680.26572900.19995519X-RAY DIFFRACTION100
6.4168-7.06090.22922880.18925467X-RAY DIFFRACTION100
7.0609-8.07870.19542930.17095551X-RAY DIFFRACTION100
8.0787-10.16360.21012920.14825532X-RAY DIFFRACTION100
10.1636-49.20180.24232850.19965437X-RAY DIFFRACTION95

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