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Structure of cobinamide-bound BtuF mutant W66L, 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 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.28 α = 90 b = 90.46 β = 110.74 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 1.5 19.67 96.77 11.04 3 89061
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 1.5 19.67 84607 4454 96.77 0.19772 0.1961 0.1956 0.22875 0.2278 RANDOM 24.9
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] 1.13 0.18 -1.05 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.546 r_dihedral_angle_4_deg 18.446 r_dihedral_angle_3_deg 13.204 r_long_range_B_other 7.605 r_long_range_B_refined 7.604 r_dihedral_angle_1_deg 6.715 r_scangle_other 4.667 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 3.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.546 r_dihedral_angle_4_deg 18.446 r_dihedral_angle_3_deg 13.204 r_long_range_B_other 7.605 r_long_range_B_refined 7.604 r_dihedral_angle_1_deg 6.715 r_scangle_other 4.667 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 3.077 r_scbond_other 3.073 r_angle_refined_deg 2.423 r_mcbond_it 2.167 r_mcbond_other 2.162 r_angle_other_deg 0.953 r_chiral_restr 0.254 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 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 3539 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XSCALE data scaling PHENIX phasing