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BtuJ1 - Bacteroides thetaiotaomicron B12 scavenging protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 29% w/v PEG, 0.2M sodium citrate pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.69 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.891 α = 90 b = 51.416 β = 131.789 c = 108.757 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 100 PIXEL DECTRIS EIGER X 9M 2024-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 1.6 81.09 82 0.2 0.2 0.1 0.968 1.7 4.4 66258 13.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 0.381
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.603 81.09 66257 3429 82.048 0.19 0.1886 0.1886 0.2132 0.2137 20.543
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] 0.128 0.159 -1.048 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.039 r_dihedral_angle_3_deg 11.096 r_dihedral_angle_2_deg 9.459 r_dihedral_angle_1_deg 8.647 r_lrange_it 7.503 r_lrange_other 6.593 r_angle_refined_deg 2.351 r_scangle_it 2.295 r_scangle_other 2.294 r_mcangle_it 2.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.039 r_dihedral_angle_3_deg 11.096 r_dihedral_angle_2_deg 9.459 r_dihedral_angle_1_deg 8.647 r_lrange_it 7.503 r_lrange_other 6.593 r_angle_refined_deg 2.351 r_scangle_it 2.295 r_scangle_other 2.294 r_mcangle_it 2.044 r_mcangle_other 2.044 r_angle_other_deg 1.401 r_scbond_it 1.388 r_scbond_other 1.388 r_mcbond_it 1.172 r_mcbond_other 1.172 r_nbtor_refined 0.149 r_nbd_refined 0.142 r_symmetry_nbd_other 0.115 r_chiral_restr 0.111 r_nbd_other 0.111 r_symmetry_xyhbond_nbd_refined 0.1 r_symmetry_nbd_refined 0.083 r_xyhbond_nbd_refined 0.08 r_ncsr_local_group_1 0.066 r_symmetry_nbtor_other 0.059 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.01 r_bond_other_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3674 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing