5VYT

Crystal structure of the WbkC N-formyltransferase (F142A variant) from Brucella melitensis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627713-15% PEG5000, 2% glycerol, 5 mM GDP-perosamine, 5 mM folinic acid, 100 mM MES
Crystal Properties
Matthews coefficientSolvent content
2.3146.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.315α = 90
b = 68.021β = 90
c = 236.035γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.25096.50.0930.0937.16.354309
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)
12.22.380.60.4120.4121.82.2

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 REPLACEMENTTHROUGHOUT5vyr2.25051622268796.560.205370.202130.26779RANDOM28.907
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]
-0.060.44-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.202
r_dihedral_angle_4_deg16.666
r_dihedral_angle_3_deg16.316
r_dihedral_angle_1_deg6.639
r_long_range_B_refined5.135
r_long_range_B_other5.114
r_scangle_other3.488
r_mcangle_it2.998
r_mcangle_other2.997
r_scbond_it2.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.202
r_dihedral_angle_4_deg16.666
r_dihedral_angle_3_deg16.316
r_dihedral_angle_1_deg6.639
r_long_range_B_refined5.135
r_long_range_B_other5.114
r_scangle_other3.488
r_mcangle_it2.998
r_mcangle_other2.997
r_scbond_it2.181
r_scbond_other2.178
r_mcbond_it1.863
r_mcbond_other1.857
r_angle_refined_deg1.664
r_angle_other_deg0.992
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7950
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing