5F12

WrbA in complex with FMN under crystallization conditions of WrbA-FMN-BQ structure (4YQE)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B6I 

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
1.8834.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.75α = 90
b = 60.75β = 90
c = 169.02γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

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
11.55099.90.111.78.45177251696
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)
11.51.5999.40.792.218.5

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 REPLACEMENTTHROUGHOUT3b6i1.542.9649068262899.850.17940.17790.2053RANDOM21.533
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_deg34.081
r_dihedral_angle_3_deg11.774
r_dihedral_angle_4_deg11.37
r_dihedral_angle_1_deg6.943
r_angle_refined_deg2.004
r_angle_other_deg1.388
r_chiral_restr0.125
r_bond_refined_d0.02
r_gen_planes_refined0.016
r_bond_other_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.081
r_dihedral_angle_3_deg11.774
r_dihedral_angle_4_deg11.37
r_dihedral_angle_1_deg6.943
r_angle_refined_deg2.004
r_angle_other_deg1.388
r_chiral_restr0.125
r_bond_refined_d0.02
r_gen_planes_refined0.016
r_bond_other_d0.007
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2811
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms62

Software

Software
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
BALBESphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
XSCALEdata scaling