5M3B

Structure of cobinamide-bound BtuF mutant W66L, 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
2.3347.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.28α = 90
b = 90.46β = 110.74
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
11.519.6796.7711.04389061

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 REPLACEMENTTHROUGHOUT5M291.519.6784607445496.770.197720.19610.22875RANDOM24.9
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]
1.130.18-1.05-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.546
r_dihedral_angle_4_deg18.446
r_dihedral_angle_3_deg13.204
r_long_range_B_other7.605
r_long_range_B_refined7.604
r_dihedral_angle_1_deg6.715
r_scangle_other4.667
r_mcangle_it3.371
r_mcangle_other3.371
r_scbond_it3.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.546
r_dihedral_angle_4_deg18.446
r_dihedral_angle_3_deg13.204
r_long_range_B_other7.605
r_long_range_B_refined7.604
r_dihedral_angle_1_deg6.715
r_scangle_other4.667
r_mcangle_it3.371
r_mcangle_other3.371
r_scbond_it3.077
r_scbond_other3.073
r_angle_refined_deg2.423
r_mcbond_it2.167
r_mcbond_other2.162
r_angle_other_deg0.953
r_chiral_restr0.254
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.001
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 Atoms3539
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XSCALEdata scaling
PHENIXphasing