5VYU

Crystal structure of the WbkC N-formyltransferase from Brucella melitensis in complex with GDP-perosaminea and N-10-formyltetrahydrofolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VYR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627713-155 PEG-5000, 2% GLYCEROL, 5 mM GDP-perosamine, 5 mM folinic acid
Crystal Properties
Matthews coefficientSolvent content
2.2545.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.835α = 90
b = 66.835β = 90
c = 235.947γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-11-09MSINGLE 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
12.25098.40.0910.09110827823
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)
12.22.396.30.4010.4012.63.6

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 REPLACEMENTTHROUGHOUT5vyr2.25026412141198.580.209080.206120.2642RANDOM21.689
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]
0.480.48-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.252
r_dihedral_angle_4_deg16.356
r_dihedral_angle_3_deg16.209
r_dihedral_angle_1_deg7.058
r_long_range_B_refined4.585
r_long_range_B_other4.581
r_scangle_other2.787
r_mcangle_it2.348
r_mcangle_other2.345
r_scbond_it1.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.252
r_dihedral_angle_4_deg16.356
r_dihedral_angle_3_deg16.209
r_dihedral_angle_1_deg7.058
r_long_range_B_refined4.585
r_long_range_B_other4.581
r_scangle_other2.787
r_mcangle_it2.348
r_mcangle_other2.345
r_scbond_it1.711
r_scbond_other1.694
r_angle_refined_deg1.614
r_mcbond_it1.438
r_mcbond_other1.431
r_angle_other_deg1.016
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3850
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing