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Crystal structure of BfrB protein from Bacteroides fragilis NCTC 9343
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 1.6M ammonium sulphate, 100mM sodium acetate, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.79 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.465 α = 90 b = 42.311 β = 95.49 c = 110.392 γ = 90
Symmetry Space Group I 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 100 PIXEL DECTRIS EIGER X 16M 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.77 38.44 96.9 0.176 0.141 0.983 4.2 3.9 40527 13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.81 75.4 1.458 1.078 0.346 0.5 2.5
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 6EWM 1.77 38.47 38371 2095 96.66 0.2082 0.2055 0.2113 0.25913 0.2693 RANDOM 19.359
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] 3.36 0.81 -2.99 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 14.788 r_dihedral_angle_3_deg 13.244 r_dihedral_angle_1_deg 7.927 r_long_range_B_refined 4.972 r_long_range_B_other 4.251 r_scangle_other 2.608 r_mcangle_other 1.748 r_mcangle_it 1.747 r_scbond_it 1.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 14.788 r_dihedral_angle_3_deg 13.244 r_dihedral_angle_1_deg 7.927 r_long_range_B_refined 4.972 r_long_range_B_other 4.251 r_scangle_other 2.608 r_mcangle_other 1.748 r_mcangle_it 1.747 r_scbond_it 1.704 r_scbond_other 1.624 r_angle_refined_deg 1.461 r_angle_other_deg 1.267 r_mcbond_it 1.11 r_mcbond_other 1.1 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 2672 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing