4YQE

Crystal structure of E. coli WrbA in complex with benzoquinone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52950.1 M MES/Imidazol, 12.5 % PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol
Crystal Properties
Matthews coefficientSolvent content
1.9235.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.179α = 90
b = 61.179β = 90
c = 169.992γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3342.599.90.04918.025.6314202514193920.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.331.4199.80.6572.36

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2RG11.3342.571491376399.920.12660.12480.1608RANDOM21.479
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.375
r_sphericity_free28.296
r_dihedral_angle_4_deg12.897
r_sphericity_bonded11.336
r_dihedral_angle_3_deg10.971
r_dihedral_angle_1_deg5.576
r_rigid_bond_restr3.235
r_mcangle_it2.998
r_mcbond_it2.511
r_mcbond_other2.502
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.375
r_sphericity_free28.296
r_dihedral_angle_4_deg12.897
r_sphericity_bonded11.336
r_dihedral_angle_3_deg10.971
r_dihedral_angle_1_deg5.576
r_rigid_bond_restr3.235
r_mcangle_it2.998
r_mcbond_it2.511
r_mcbond_other2.502
r_angle_refined_deg1.642
r_angle_other_deg1.117
r_chiral_restr0.094
r_gen_planes_refined0.015
r_bond_refined_d0.013
r_bond_other_d0.005
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2806
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
XSCALEdata scaling