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- PDB-4xsz: Crystal structure of CBR 9393 bound to Escherichia coli RNA polym... -

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Basic information

Entry
Database: PDB / ID: 4xsz
TitleCrystal structure of CBR 9393 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 / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / 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 / response to heat ...sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / 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 / 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 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 ...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 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 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 / 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 / Sigma-70 factors family signature 1. / 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 / Helix Hairpins / 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 / Helix non-globular / 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 / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-42U / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.683 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 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 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)860,51920
Polymers859,34112
Non-polymers1,1778
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)430,25910
Polymers429,6716
Non-polymers5894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37710 Å2
ΔGint-181 kcal/mol
Surface area153380 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)430,25910
Polymers429,6716
Non-polymers5894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37130 Å2
ΔGint-176 kcal/mol
Surface area156030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.444, 206.331, 309.607
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(-0.382031, -0.003792, -0.924142), (-0.042633, -0.998855, 0.021722), (-0.923165, 0.047698, 0.381432)-69.613602, -221.403, -42.349602
2given(-0.443764, 0.035884, -0.895425), (-0.070062, -0.997529, -0.005254), (-0.893401, 0.060404, 0.445181)-66.818001, -225.410995, -33.302799
3given(-0.337506, 0.090803, -0.936934), (-0.090204, -0.993876, -0.063828), (-0.936991, 0.062973, 0.34363)-54.6488, -231.373993, -44.6022
4given(-0.332243, 0.111751, -0.93655), (-0.098457, -0.991641, -0.083397), (-0.938041, 0.064502, 0.340468)-51.489601, -233.531998, -44.679699
5given(-0.376049, -0.002967, -0.926595), (-0.048308, -0.998572, 0.022802), (-0.92534, 0.053336, 0.375369)-69.262802, -221.75, -42.033798
6given(-0.428465, -0.01722, -0.903394), (-0.01378, -0.999578, 0.025589), (-0.903453, 0.023413, 0.428046)-73.672997, -219.076004, -42.542301
7given(-0.379774, -2.536, -0.903394), (-0.038989, -0.999111, 0.016009), (-0.924257, 0.042148, 0.379436)-68.754303, -221.546997, -43.572399
8given(-0.39702, 0.005585, -0.917793), (-0.025285, -0.999668, 0.004855), (-0.917462, 0.025134, 0.39703)-68.6073, -221.531998, -44.6595
9given(-0.366788, 0.049073, -0.929009), (0.053129, -0.995873, -0.073581), (-0.928786, -0.076346, 0.362667)-61.457699, -226.110001, -65.714996
10given(-0.41274, -0.01507, -0.910724), (-0.007277, -0.999777, 0.019842), (-0.91082, 0.014817, 0.412538)-72.291496, -219.626999, -45.097301
11given(-0.372124, 0.01162, -0.92811), (-0.053981, -0.9985, 0.009142), (-0.926612, 0.053503, 0.372194)-66.715302, -222.889999, -42.202
12given(-0.438959, 0.036788, -0.897753), (-0.034081, -0.999124, -0.024278), (-0.89786, 0.01994, 0.439829)-69.494202, -221.397995, -42.592899
13given(-0.391953, -0.006104, -0.919965), (-0.040048, -0.998917, 0.02369), (-0.919113, 0.046129, 0.391284)-70.193604, -220.983994, -42.0611
14given(-0.382855, -0.005881, -0.92379), (-0.04862, -0.998466, 0.026507), (-0.922528, 0.055063, 0.381982)-70.026398, -221.160995, -41.588799
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 / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase 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) Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) (bacteria)
Strain: ATCC 8739 / DSM 1576 / Crooks / References: UniProt: B1IYV1, 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-42U / 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline / CBR-9393


Mass: 433.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23F4N5
#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: 3.43 Å3/Da / Density % sol: 64.12 %
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: Jul 26, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.68→40 Å / Num. obs: 113807 / % possible obs: 89.4 % / Redundancy: 18.3 % / Biso Wilson estimate: 139.86 Å2 / Rmerge(I) obs: 0.148 / Χ2: 1.392 / Net I/av σ(I): 15.068 / Net I/σ(I): 5.5 / Num. measured all: 2086355
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.68-3.8316.8108640.94786.4
3.83-3.9918.2110120.96487.6
3.99-4.1718.9110960.99987.9
4.17-4.3919.1111341.073880.841
4.39-4.6619.3110911.1487.90.574
4.66-5.0219.3111881.1888.10.429
5.02-5.5219113541.19689.50.358
5.52-6.3218.6117491.28191.90.267
6.32-7.9518120461.98393.60.137
7.95-4016.3122733.17992.70.052

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ljz


Resolution: 3.683→39.934 Å / FOM work R set: 0.7167 / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2861 5685 5.02 %
Rwork0.24 107492 -
obs0.2424 113177 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.43 Å2 / Biso mean: 97.91 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: final / Resolution: 3.683→39.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55676 0 68 0 55744
Biso mean--83.79 --
Num. residues----7078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456555
X-RAY DIFFRACTIONf_angle_d1.01376323
X-RAY DIFFRACTIONf_chiral_restr0.0728680
X-RAY DIFFRACTIONf_plane_restr0.00410001
X-RAY DIFFRACTIONf_dihedral_angle_d17.80321826
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C8085X-RAY DIFFRACTIONPOSITIONAL0.015
12I8085X-RAY DIFFRACTIONPOSITIONAL0.015
21C1315X-RAY DIFFRACTIONPOSITIONAL0.027
22I1315X-RAY DIFFRACTIONPOSITIONAL0.027
31C1470X-RAY DIFFRACTIONPOSITIONAL0.018
32I1470X-RAY DIFFRACTIONPOSITIONAL0.018
41C912X-RAY DIFFRACTIONPOSITIONAL0.008
42I912X-RAY DIFFRACTIONPOSITIONAL0.008
51C549X-RAY DIFFRACTIONPOSITIONAL0.011
52I549X-RAY DIFFRACTIONPOSITIONAL0.011
61C1414X-RAY DIFFRACTIONPOSITIONAL0.025
62I1414X-RAY DIFFRACTIONPOSITIONAL0.025
71C835X-RAY DIFFRACTIONPOSITIONAL0.013
72I835X-RAY DIFFRACTIONPOSITIONAL0.013
81C4027X-RAY DIFFRACTIONPOSITIONAL0.024
82I4027X-RAY DIFFRACTIONPOSITIONAL0.024
91F1608X-RAY DIFFRACTIONPOSITIONAL0.018
92L1608X-RAY DIFFRACTIONPOSITIONAL0.018
101F836X-RAY DIFFRACTIONPOSITIONAL0.017
102L836X-RAY DIFFRACTIONPOSITIONAL0.017
111A1725X-RAY DIFFRACTIONPOSITIONAL0.007
112G1725X-RAY DIFFRACTIONPOSITIONAL0.007
121B1632X-RAY DIFFRACTIONPOSITIONAL0.008
122H1632X-RAY DIFFRACTIONPOSITIONAL0.008
131D2039X-RAY DIFFRACTIONPOSITIONAL0.025
132J2039X-RAY DIFFRACTIONPOSITIONAL0.025
141D511X-RAY DIFFRACTIONPOSITIONAL0.011
142J511X-RAY DIFFRACTIONPOSITIONAL0.011
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 (%)
3.6827-3.72450.39031600.35172680284068
3.7245-3.76830.42131630.34163372353583
3.7683-3.81420.41061810.33083398357986
3.8142-3.86250.37181920.31333493368587
3.8625-3.91320.42991790.32063540371987
3.9132-3.96680.40311780.32173520369888
3.9668-4.02340.36831930.31123441363487
4.0234-4.08340.3732000.30473527372788
4.0834-4.14720.33851910.28033530372188
4.1472-4.21510.35751940.29673505369988
4.2151-4.28770.35651950.28453533372888
4.2877-4.36560.36712040.27723492369688
4.3656-4.44940.33841860.26463530371688
4.4494-4.54010.33761770.25743532370987
4.5401-4.63870.31421760.25333534371088
4.6387-4.74640.31281950.24533495369087
4.7464-4.86490.35651880.2483576376488
4.8649-4.99620.34351920.24153529372188
4.9962-5.14290.33251960.24133585378189
5.1429-5.30860.31671790.23023629380890
5.3086-5.49790.3121760.22683646382290
5.4979-5.71740.30491740.233757393191
5.7174-5.97680.29182280.22873665389392
5.9768-6.29070.27951760.22743845402193
6.2907-6.68320.29091820.22433803398593
6.6832-7.19640.28571960.22573832402894
7.1964-7.91550.23882060.20573854406094
7.9155-9.04930.22792020.19153844404693
9.0493-11.35750.17282090.17793850405993
11.3575-39.93650.24632170.25323955417292

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