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- PDB-4zqx: A revised partiality model and post-refinement algorithm for X-ra... -

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Basic information

Entry
Database: PDB / ID: 4zqx
TitleA revised partiality model and post-refinement algorithm for X-ray free-electron laser data
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / post-refinement / free-electron laser / partiality
Function / homologyCypovirus polyhedrin / Cypovirus polyhedrin / ATP binding / ADENOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesUranotaenia sapphirina cypovirus
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsGinn, H.M. / Brewster, A.S. / Hattne, J. / Evans, G. / Wagner, A. / Grimes, J. / Sauter, N.K. / Sutton, G. / Stuart, D.I.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000099 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
Wellcome Trust075491/04 United Kingdom
National Institutes of HealthGM095887 United Kingdom
National Institutes of HealthGM102520 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: A revised partiality model and post-refinement algorithm for X-ray free-electron laser data.
Authors: Ginn, H.M. / Brewster, A.S. / Hattne, J. / Evans, G. / Wagner, A. / Grimes, J.M. / Sauter, N.K. / Sutton, G. / Stuart, D.I.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4793
Polymers26,9481
Non-polymers5312
Water2,504139
1
A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4379
Polymers80,8433
Non-polymers1,5946
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area12000 Å2
ΔGint-77 kcal/mol
Surface area31360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.100, 106.100, 106.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-480-

HOH

21A-532-

HOH

31A-537-

HOH

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Components

#1: Protein Polyhedrin


Mass: 26947.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Uranotaenia sapphirina cypovirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5EK29
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.55 %
Crystal growTemperature: 300 K / Method: in cell / Details: Form naturally within cells

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Mar 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.46→25.1 Å / Num. all: 34369 / Num. obs: 34369 / % possible obs: 99.5 % / Redundancy: 45.4 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
cctbx.xfeldata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S1L

4s1l


Resolution: 1.46→25.008 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.153 1720 5.01 %
Rwork0.1077 --
obs0.1101 34360 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→25.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 32 139 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082057
X-RAY DIFFRACTIONf_angle_d1.2762806
X-RAY DIFFRACTIONf_dihedral_angle_d14.113789
X-RAY DIFFRACTIONf_chiral_restr0.075289
X-RAY DIFFRACTIONf_plane_restr0.006371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4602-1.50310.33481270.28592556X-RAY DIFFRACTION95
1.5031-1.55160.31971360.24132710X-RAY DIFFRACTION100
1.5516-1.60710.28861310.19092716X-RAY DIFFRACTION100
1.6071-1.67140.26221360.1662743X-RAY DIFFRACTION100
1.6714-1.74750.26361500.14322687X-RAY DIFFRACTION100
1.7475-1.83960.2041350.12362735X-RAY DIFFRACTION100
1.8396-1.95480.17011370.09992731X-RAY DIFFRACTION100
1.9548-2.10560.16231690.08772683X-RAY DIFFRACTION100
2.1056-2.31740.14681600.08512727X-RAY DIFFRACTION100
2.3174-2.65240.14871530.0952740X-RAY DIFFRACTION100
2.6524-3.34050.15681390.10992772X-RAY DIFFRACTION100
3.3405-25.01170.12941470.10512840X-RAY DIFFRACTION100

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