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Bacteroides thetaiotaomicron surface lipoprotein bound to cyanocobalamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Lithium sulphate, 0.1M Tris pH 8.5, 1.26 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.93 57.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.315 α = 90 b = 59.078 β = 103.865 c = 101.544 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2019-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96858 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 1.72 59.08 99.4 0.108 0.147 0.099 0.988 6 3.5 97918
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 1.72 1.75 0.736 0.999 0.672 0.557 3.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DSM 1.72 55.072 97856 4849 99.455 0.181 0.1787 0.1787 0.2227 0.2228 19.783
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] 0.363 0.455 0.09 -0.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.543 r_dihedral_angle_4_deg 20.191 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_1_deg 7.815 r_lrange_it 4.094 r_lrange_other 3.622 r_scangle_it 2.961 r_scangle_other 2.936 r_scbond_it 2.429 r_scbond_other 2.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.543 r_dihedral_angle_4_deg 20.191 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_1_deg 7.815 r_lrange_it 4.094 r_lrange_other 3.622 r_scangle_it 2.961 r_scangle_other 2.936 r_scbond_it 2.429 r_scbond_other 2.417 r_mcangle_it 2.384 r_mcangle_other 2.384 r_mcbond_it 1.896 r_mcbond_other 1.891 r_angle_refined_deg 1.694 r_rigid_bond_restr 1.356 r_angle_other_deg 1.274 r_symmetry_nbd_refined 0.258 r_nbd_other 0.212 r_symmetry_nbd_other 0.179 r_nbd_refined 0.177 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.074 r_ncsr_local_group_1 0.067 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5480 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing