5M2Q

Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M29 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15PEG3350 HEPES pH 7 Tryptone
Crystal Properties
Matthews coefficientSolvent content
2.3347.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.56α = 90
b = 90.67β = 110.87
c = 50.81γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123PIXELDECTRIS PILATUS 6M-F2014-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.97794SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.719.7196.2711.053.161170

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 REPLACEMENTTHROUGHOUT5M291.719.7158109306096.270.210870.208860.24923RANDOM33.948
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]
-0.24-0.340.070.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.746
r_dihedral_angle_4_deg21.86
r_dihedral_angle_3_deg15.081
r_long_range_B_refined8.55
r_long_range_B_other8.549
r_dihedral_angle_1_deg6.593
r_scangle_other3.532
r_mcangle_it2.849
r_mcangle_other2.849
r_scbond_it2.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.746
r_dihedral_angle_4_deg21.86
r_dihedral_angle_3_deg15.081
r_long_range_B_refined8.55
r_long_range_B_other8.549
r_dihedral_angle_1_deg6.593
r_scangle_other3.532
r_mcangle_it2.849
r_mcangle_other2.849
r_scbond_it2.31
r_scbond_other2.31
r_angle_refined_deg2.308
r_mcbond_it1.745
r_mcbond_other1.739
r_angle_other_deg0.898
r_chiral_restr0.194
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms3532
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XSCALEdata scaling
PHENIXphasing