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- PDB-4xsx: Crystal structure of CBR 703 bound to Escherichia coli RNA polyme... -

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Basic information

Entry
Database: PDB / ID: 4xsx
TitleCrystal structure of CBR 703 bound to Escherichia coli RNA polymerase holoenzyme
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
Keywordstranscription/antibiotic / bacterial RNA polymerase antibiotic complex / transcription-antibiotic complex
Function / homology
Function and homology information


sigma factor antagonist complex / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat ...sigma factor antagonist complex / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein dimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 ...Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, RBP11-like subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Sigma-70 factors family signature 1. / DNA-directed RNA polymerase, insert domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Helix Hairpins / : / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / Helix non-globular / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / 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
Similarity search - Domain/homology
Chem-42S / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O139:H28 (bacteria)
Citrobacter koseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.708 Å
AuthorsBae, B. / Darst, S.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.
Authors: Bae, B. / Nayak, D. / Ray, A. / Mustaev, A. / Landick, R. / Darst, S.A.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Mar 23, 2016Group: Other
Revision 1.4Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 RpoD
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)860,21220
Polymers859,34112
Non-polymers8718
Water00
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 RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,10610
Polymers429,6716
Non-polymers4354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36980 Å2
ΔGint-176 kcal/mol
Surface area155180 Å2
MethodPISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,10610
Polymers429,6716
Non-polymers4354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36740 Å2
ΔGint-174 kcal/mol
Surface area157360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.025, 206.914, 310.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resseq 3:30 or resseq 140:150 or resseq...
21(chain I and (resseq 3:30 or resseq 140:150 or resseq...
12chain C and (resseq 31:139 or resseq 456:512)
22chain I and (resseq 31:139 or resseq 456:512)
13chain C and (resseq 151:225 or resseq 340:444)
23chain I and (resseq 151:225 or resseq 340:444)
14chain C and resseq 226:339
24chain I and resseq 226:339
15chain C and resseq 714:785
25chain I and resseq 714:785
16(chain C and (resseq 833:937 or resseq 1040:1055)) or (chain F and resseq 551:612)
26(chain I and (resseq 833:937 or resseq 1040:1055)) or (chain L and resseq 551:612)
17chain C and resseq 938:1039
27chain I and resseq 938:1039
18(chain C and resseq 1296:1342) or (chain D and (resseq...
28(chain I and resseq 1296:1342) or (chain J and (resseq...
19chain F and (resseq 128:167 or resseq 212:236 or resseq 242:374)
29chain L and (resseq 128:167 or resseq 212:236 or resseq 242:374)
110chain F and resseq 445:550
210chain L and resseq 445:550
111chain A and resseq 9:231
211chain G and resseq 9:231
112chain B and resseq 9:234
212chain H and resseq 9:234
113chain D and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)
213chain J and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)
114chain D and resseq 1151:1215
214chain J and resseq 1151:1215

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain C and (resseq 3:30 or resseq 140:150 or resseq...C3 - 30
121(chain C and (resseq 3:30 or resseq 140:150 or resseq...C140 - 150
131(chain C and (resseq 3:30 or resseq 140:150 or resseq...C445 - 455
141(chain C and (resseq 3:30 or resseq 140:150 or resseq...C513 - 713
151(chain C and (resseq 3:30 or resseq 140:150 or resseq...C786 - 832
161(chain C and (resseq 3:30 or resseq 140:150 or resseq...C1056 - 1295
211(chain I and (resseq 3:30 or resseq 140:150 or resseq...I3 - 30
221(chain I and (resseq 3:30 or resseq 140:150 or resseq...I140 - 150
231(chain I and (resseq 3:30 or resseq 140:150 or resseq...I445 - 455
241(chain I and (resseq 3:30 or resseq 140:150 or resseq...I513 - 713
251(chain I and (resseq 3:30 or resseq 140:150 or resseq...I786 - 832
261(chain I and (resseq 3:30 or resseq 140:150 or resseq...I1056 - 1295
112chain C and (resseq 31:139 or resseq 456:512)C31 - 139
122chain C and (resseq 31:139 or resseq 456:512)C456 - 512
212chain I and (resseq 31:139 or resseq 456:512)I31 - 139
222chain I and (resseq 31:139 or resseq 456:512)I456 - 512
113chain C and (resseq 151:225 or resseq 340:444)C151 - 225
123chain C and (resseq 151:225 or resseq 340:444)C340 - 444
213chain I and (resseq 151:225 or resseq 340:444)I151 - 225
223chain I and (resseq 151:225 or resseq 340:444)I340 - 444
114chain C and resseq 226:339C226 - 339
214chain I and resseq 226:339I226 - 339
115chain C and resseq 714:785C714 - 785
215chain I and resseq 714:785I714 - 785
116(chain C and (resseq 833:937 or resseq 1040:1055)) or (chain F and resseq 551:612)C833 - 937
126(chain C and (resseq 833:937 or resseq 1040:1055)) or (chain F and resseq 551:612)C1040 - 1055
216(chain I and (resseq 833:937 or resseq 1040:1055)) or (chain L and resseq 551:612)I833 - 937
226(chain I and (resseq 833:937 or resseq 1040:1055)) or (chain L and resseq 551:612)I1040 - 1055
117chain C and resseq 938:1039C938 - 1039
217chain I and resseq 938:1039I938 - 1039
118(chain C and resseq 1296:1342) or (chain D and (resseq...C1296 - 1342
218(chain I and resseq 1296:1342) or (chain J and (resseq...I1296 - 1342
119chain F and (resseq 128:167 or resseq 212:236 or resseq 242:374)F128 - 167
129chain F and (resseq 128:167 or resseq 212:236 or resseq 242:374)F212 - 236
139chain F and (resseq 128:167 or resseq 212:236 or resseq 242:374)F242 - 374
219chain L and (resseq 128:167 or resseq 212:236 or resseq 242:374)L128 - 167
229chain L and (resseq 128:167 or resseq 212:236 or resseq 242:374)L212 - 236
239chain L and (resseq 128:167 or resseq 212:236 or resseq 242:374)L242 - 374
1110chain F and resseq 445:550F445 - 550
2110chain L and resseq 445:550L445 - 550
1111chain A and resseq 9:231A9 - 231
2111chain G and resseq 9:231G9 - 231
1112chain B and resseq 9:234B9 - 234
2112chain H and resseq 9:234H9 - 234
1113chain D and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)D809 - 931
1213chain D and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)D1127 - 1150
1313chain D and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)D1216 - 1344
1413chain D and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)D1410
2113chain J and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)J809 - 931
2213chain J and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)J1127 - 1150
2313chain J and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)J1216 - 1344
2413chain J and (resseq 809:931 or resseq 1127:1150 or resseq 1216:1344 or resseq 1410)J1410
1114chain D and resseq 1151:1215D0
2114chain J and resseq 1151:1215J0

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(-0.395366, -0.007365, -0.918494), (-0.040737, -0.998843, 0.025544), (-0.91762, 0.047516, 0.394608)-70.431198, -221.462006, -41.549801
2given(-0.454573, 0.033081, -0.890095), (-0.068544, -0.997646, -0.002073), (-0.888068, 0.060069, 0.45577)-67.219002, -225.580994, -32.7393
3given(-0.340239, 0.081148, -0.936831), (-0.082735, -0.994989, -0.056138), (-0.936692, 0.058408, 0.345248)-55.787899, -230.899002, -45.7715
4given(-0.322971, 0.105188, -0.940545), (-0.095619, -0.992346, -0.078146), (-0.941566, 0.064695, 0.330557)-52.098099, -233.546997, -46.561298
5given(-0.398357, -0.01431, -0.917119), (-0.040386, -0.998635, 0.033124), (-0.916341, 0.050234, 0.397235)-71.676598, -220.830994, -40.822498
6given(-0.431944, -0.016089, -0.901757), (-0.015007, -0.999574, 0.025023), (-0.901776, 0.024341, 0.431519)-73.190399, -219.733994, -42.262798
7given(-0.397472, -0.006529, -0.917591), (-0.052397, -0.998182, 0.029799), (-0.916117, 0.059923, 0.396407)-70.3834, -222.257004, -39.141201
8given(-0.402528, -0.003051, -0.915403), (-0.022186, -0.999668, 0.013087), (-0.915139, 0.025577, 0.402326)-69.898804, -221.345993, -44.238899
9given(-0.388453, 0.039351, -0.920628), (0.053859, -0.99641, -0.065316), (-0.919893, -0.074957, 0.384939)-62.742199, -226.037994, -63.719799
10given(-0.415722, -0.021787, -0.909231), (0.001219, -0.999725, 0.023398), (-0.909491, 0.008618, 0.415635)-73.204399, -219.455002, -46.044899
11given(-0.403658, 0.001581, -0.914909), (-0.042364, -0.998958, 0.016964), (-0.913929, 0.045607, 0.403304)-69.713097, -221.850006, -41.132198
12given(-0.411709, -0.027181, -0.91091), (-0.035523, -0.998317, 0.045845), (-0.910623, 0.051233, 0.41005)-74.1483, -220.117996, -40.217999
13given(-0.400566, -0.011616, -0.916194), (-0.036934, -0.998902, 0.028812), (-0.915523, 0.04538, 0.399697)-71.084297, -220.953995, -41.5966
14given(-0.396681, -0.008025, -0.917922), (-0.044025, -0.998645, 0.027756), (-0.9169, 0.051421, 0.39579)-70.647102, -221.302002, -41.072399
Detailsbiological unit is the same as asym.

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Components

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

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


Mass: 26459.125 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / References: UniProt: A7ZSI4, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 150820.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / References: UniProt: A7ZUK1, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / References: UniProt: A7ZUK2, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (bacteria)
Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / References: UniProt: A8ARN6, DNA-directed RNA polymerase

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Protein , 1 types, 2 molecules FL

#5: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 60315.254 Da / Num. of mol.: 2 / Fragment: unp residues 92-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Plasmid: pEcrpoA(-X234-241H)BCZ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T-X234-241H / References: UniProt: P00579

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Non-polymers , 3 types, 8 molecules

#6: Chemical ChemComp-42S / N'-hydroxy-N-phenyl-3-(trifluoromethyl)benzenecarboximidamide


Mass: 280.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11F3N2O
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES, calcium acetate, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.7→40 Å / Num. obs: 126483 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 142.32 Å2 / Rmerge(I) obs: 0.144 / Χ2: 1.609 / Net I/av σ(I): 19.466 / Net I/σ(I): 6.5 / Num. measured all: 1671904
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.7-3.8311.9124050.96199
3.83-3.9913.2125150.995100
3.99-4.1713.5125331.0581000.929
4.17-4.3913.6125611.1781000.589
4.39-4.6613.5125811.3271000.413
4.66-5.0213.5126001.4191000.329
5.02-5.5213.5126381.4641000.287
5.52-6.3213.7126941.6051000.228
6.32-7.9513.6128022.4951000.128
7.95-4012.2131543.57699.90.054

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJZ

4ljz


Resolution: 3.708→40 Å / FOM work R set: 0.7457 / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 6331 5.02 %
Rwork0.2301 119867 -
obs0.2323 126198 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 490 Å2 / Biso mean: 102.01 Å2 / Biso min: 5.62 Å2
Refinement stepCycle: final / Resolution: 3.708→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55676 0 46 0 55722
Biso mean--109.12 --
Num. residues----7078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556529
X-RAY DIFFRACTIONf_angle_d1.01576285
X-RAY DIFFRACTIONf_chiral_restr0.0728680
X-RAY DIFFRACTIONf_plane_restr0.00410001
X-RAY DIFFRACTIONf_dihedral_angle_d17.45121806
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C8074X-RAY DIFFRACTIONPOSITIONAL0.016
12I8074X-RAY DIFFRACTIONPOSITIONAL0.016
21C1315X-RAY DIFFRACTIONPOSITIONAL0.025
22I1315X-RAY DIFFRACTIONPOSITIONAL0.025
31C1470X-RAY DIFFRACTIONPOSITIONAL0.019
32I1470X-RAY DIFFRACTIONPOSITIONAL0.019
41C912X-RAY DIFFRACTIONPOSITIONAL0.009
42I912X-RAY DIFFRACTIONPOSITIONAL0.009
51C549X-RAY DIFFRACTIONPOSITIONAL0.009
52I549X-RAY DIFFRACTIONPOSITIONAL0.009
61C1414X-RAY DIFFRACTIONPOSITIONAL0.023
62I1414X-RAY DIFFRACTIONPOSITIONAL0.023
71C835X-RAY DIFFRACTIONPOSITIONAL0.017
72I835X-RAY DIFFRACTIONPOSITIONAL0.017
81C4027X-RAY DIFFRACTIONPOSITIONAL0.028
82I4027X-RAY DIFFRACTIONPOSITIONAL0.028
91F1608X-RAY DIFFRACTIONPOSITIONAL0.019
92L1608X-RAY DIFFRACTIONPOSITIONAL0.019
101F836X-RAY DIFFRACTIONPOSITIONAL0.017
102L836X-RAY DIFFRACTIONPOSITIONAL0.017
111A1725X-RAY DIFFRACTIONPOSITIONAL0.008
112G1725X-RAY DIFFRACTIONPOSITIONAL0.008
121B1632X-RAY DIFFRACTIONPOSITIONAL0.011
122H1632X-RAY DIFFRACTIONPOSITIONAL0.011
131D2039X-RAY DIFFRACTIONPOSITIONAL0.024
132J2039X-RAY DIFFRACTIONPOSITIONAL0.024
141D511X-RAY DIFFRACTIONPOSITIONAL0.01
142J511X-RAY DIFFRACTIONPOSITIONAL0.01
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 (%)
3.7082-3.75030.41831610.35342794295569
3.7503-3.79440.41381970.34913950414799
3.7944-3.84060.3732230.314739644187100
3.8406-3.88920.36282150.299140094224100
3.8892-3.94030.36842090.307839924201100
3.9403-3.99430.37191970.307140064203100
3.9943-4.05130.36182070.286640124219100
4.0513-4.11170.29942230.272539804203100
4.1117-4.17590.31882140.263140024216100
4.1759-4.24430.32962110.265740154226100
4.2443-4.31740.32072230.257639764199100
4.3174-4.39580.33142390.253539774216100
4.3958-4.48020.30522090.240540114220100
4.4802-4.57160.30832050.232140314236100
4.5716-4.67080.28572120.236140074219100
4.6708-4.77930.29812200.230340214241100
4.7793-4.89860.30092000.228540124212100
4.8986-5.03080.29562030.229940594262100
5.0308-5.17860.29672250.224940244249100
5.1786-5.34530.28762080.228140394247100
5.3453-5.53590.31671970.225940344231100
5.5359-5.75690.30421950.225340534248100
5.7569-6.01810.28852460.224340304276100
6.0181-6.33430.28941920.217140714263100
6.3343-6.72940.26631960.224740914287100
6.7294-7.24610.26012160.213740774293100
7.2461-7.97020.23342050.199941134318100
7.9702-9.11160.20692200.183141024322100
9.1116-11.43530.17732270.173241304357100
11.4353-40.0690.25032360.24834285452199

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