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Crystal structure of BfrC protein from Bacteroides fragilis NCTC 9343
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alpha fold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.02 M M Magnesium chloride hexahydrate, 0.1M HEPES at pH 7.5 and 22 % w/v Poly acrylic acid sodium salt 5100
Crystal Properties Matthews coefficient Solvent content 2.58 52.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.075 α = 90 b = 89.84 β = 90 c = 99.056 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2021-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.81 66.55 99.4 0.15 0.178 0.071 0.996 6.1 6 43116 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.84 91.6 1.421 1.8 0.871 0.372 0.7 3.9
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 alpha fold 1.81 66.55 40814 2219 99.25 0.20378 0.20122 0.1998 0.25069 0.2521 RANDOM 27.616
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] -0.86 -0.12 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.245 r_dihedral_angle_4_deg 20.871 r_dihedral_angle_3_deg 13.817 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.288 r_long_range_B_other 6.057 r_scangle_other 2.397 r_mcangle_it 2.038 r_mcangle_other 2.037 r_angle_refined_deg 1.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.245 r_dihedral_angle_4_deg 20.871 r_dihedral_angle_3_deg 13.817 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.288 r_long_range_B_other 6.057 r_scangle_other 2.397 r_mcangle_it 2.038 r_mcangle_other 2.037 r_angle_refined_deg 1.697 r_scbond_it 1.523 r_scbond_other 1.523 r_angle_other_deg 1.364 r_mcbond_it 1.201 r_mcbond_other 1.193 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 3171 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing