☰ Navigation Tabs
Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 binding protein in E.coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 HEPES sodium pH 7.0
PEG3350
Tryptone
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.15 α = 90 b = 90.56 β = 110.9 c = 50.84 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 2013-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00001 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 29.39 96.02 0.059 10.16 3.5 89615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.69 0.849
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 1N2Z 1.5 29.39 85134 4481 96.02 0.18073 0.17903 0.1883 0.21296 0.2191 RANDOM 31.424
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] 3.48 0.49 -1.93 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.372 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 12.879 r_long_range_B_other 8.908 r_long_range_B_refined 8.904 r_dihedral_angle_1_deg 6.76 r_scangle_other 5.933 r_mcangle_it 4.286 r_mcangle_other 4.286 r_scbond_it 3.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.372 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 12.879 r_long_range_B_other 8.908 r_long_range_B_refined 8.904 r_dihedral_angle_1_deg 6.76 r_scangle_other 5.933 r_mcangle_it 4.286 r_mcangle_other 4.286 r_scbond_it 3.867 r_scbond_other 3.867 r_mcbond_it 2.927 r_mcbond_other 2.921 r_angle_refined_deg 2.228 r_angle_other_deg 0.909 r_chiral_restr 0.224 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 3548 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XSCALE data scaling XDS data reduction PHENIX phasing