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Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 PEG3350
HEPES pH 7
Tryptone
Crystal Properties Matthews coefficient Solvent content 2.33 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.56 α = 90 b = 90.67 β = 110.87 c = 50.81 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 PIXEL DECTRIS PILATUS 6M-F 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97794 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 19.71 96.27 11.05 3.1 61170
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5M29 1.7 19.71 58109 3060 96.27 0.21087 0.20886 0.2169 0.24923 0.2548 RANDOM 33.948
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 -0.34 0.07 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.746 r_dihedral_angle_4_deg 21.86 r_dihedral_angle_3_deg 15.081 r_long_range_B_refined 8.55 r_long_range_B_other 8.549 r_dihedral_angle_1_deg 6.593 r_scangle_other 3.532 r_mcangle_it 2.849 r_mcangle_other 2.849 r_scbond_it 2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.746 r_dihedral_angle_4_deg 21.86 r_dihedral_angle_3_deg 15.081 r_long_range_B_refined 8.55 r_long_range_B_other 8.549 r_dihedral_angle_1_deg 6.593 r_scangle_other 3.532 r_mcangle_it 2.849 r_mcangle_other 2.849 r_scbond_it 2.31 r_scbond_other 2.31 r_angle_refined_deg 2.308 r_mcbond_it 1.745 r_mcbond_other 1.739 r_angle_other_deg 0.898 r_chiral_restr 0.194 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 3532 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XSCALE data scaling PHENIX phasing