4OUQ

Crystal structure of a DUF4783 family protein (BF1468) from Bacteroides fragilis YCH46 at 1.55 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP927730.0% polyethylene glycol 6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
1.9536.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.467α = 90
b = 48.316β = 90
c = 49.322γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MRhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator2012-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-2SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.5521.96596.40.0649.23.21396713967
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5997.70.6450.6451.631032

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.5521.9651393069195.580.20090.1990.2391RANDOM26.1654
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]
-0.540.91-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.489
r_dihedral_angle_4_deg19.837
r_dihedral_angle_3_deg13.108
r_dihedral_angle_1_deg5.25
r_mcangle_it3.505
r_mcbond_it2.879
r_mcbond_other2.875
r_angle_refined_deg1.359
r_angle_other_deg0.758
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.489
r_dihedral_angle_4_deg19.837
r_dihedral_angle_3_deg13.108
r_dihedral_angle_1_deg5.25
r_mcangle_it3.505
r_mcbond_it2.879
r_mcbond_other2.875
r_angle_refined_deg1.359
r_angle_other_deg0.758
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms812
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction