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lipoprotein BT2095 from Bacteroides thetaiotamicron bound to cyanocobalamin CnCbl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Optimised from Index H8, 0.1MgFormate 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.77 α = 90 b = 131.04 β = 90 c = 179.38 γ = 90
Symmetry Space Group P 21 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 EIGER2 XE 16M 2021-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9794 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 74.7 99.4 0.06 0.99 11.8 13.2 54678
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 2.6 2.68 0.66 1.1
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 FREE R-VALUE 2.6 74.123 54607 2675 99.253 0.221 0.2182 0.2183 0.276 0.2761 71.314
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] -3.316 4.184 -0.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.463 r_dihedral_angle_6_deg 15.96 r_dihedral_angle_2_deg 13.158 r_lrange_it 10.071 r_lrange_other 10.071 r_dihedral_angle_1_deg 9.311 r_scangle_it 8.54 r_scangle_other 8.539 r_mcangle_it 7.744 r_mcangle_other 7.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.463 r_dihedral_angle_6_deg 15.96 r_dihedral_angle_2_deg 13.158 r_lrange_it 10.071 r_lrange_other 10.071 r_dihedral_angle_1_deg 9.311 r_scangle_it 8.54 r_scangle_other 8.539 r_mcangle_it 7.744 r_mcangle_other 7.744 r_scbond_it 5.969 r_scbond_other 5.969 r_mcbond_it 5.535 r_mcbond_other 5.534 r_angle_refined_deg 2.466 r_angle_other_deg 0.896 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_refined 0.183 r_nbd_other 0.177 r_nbd_refined 0.174 r_nbtor_refined 0.17 r_symmetry_nbd_other 0.166 r_symmetry_xyhbond_nbd_refined 0.154 r_chiral_restr 0.132 r_ncsr_local_group_3 0.117 r_ncsr_local_group_2 0.116 r_ncsr_local_group_1 0.111 r_ncsr_local_group_6 0.108 r_ncsr_local_group_4 0.106 r_ncsr_local_group_5 0.094 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.014 r_symmetry_xyhbond_nbd_other 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10619 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 372
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling PHASER phasing