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Bacteroides thetaiotaomicron surface lipoprotein BT1954 bound to adenosylcobalamin
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 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.723 α = 90 b = 58.709 β = 104.132 c = 101.894 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 EIGER X 16M 2021-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.89843 Diamond I03
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 2.3 70.28 100 0.231 0.273 0.144 0.984 5.1 6.8 41492
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 2.3 2.38 0.957 1.142 0.617 0.696 6.5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DSM 2.3 70.276 41442 2001 99.906 0.225 0.2228 0.268 0.2547 33.532
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] 1.812 2.426 -3.16 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.639 r_dihedral_angle_3_deg 14.595 r_dihedral_angle_2_deg 8.848 r_dihedral_angle_1_deg 8.379 r_lrange_it 4.915 r_lrange_other 4.915 r_dihedral_angle_other_2_deg 4.236 r_scangle_it 3.459 r_scangle_other 3.459 r_mcangle_other 2.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.639 r_dihedral_angle_3_deg 14.595 r_dihedral_angle_2_deg 8.848 r_dihedral_angle_1_deg 8.379 r_lrange_it 4.915 r_lrange_other 4.915 r_dihedral_angle_other_2_deg 4.236 r_scangle_it 3.459 r_scangle_other 3.459 r_mcangle_other 2.968 r_mcangle_it 2.961 r_scbond_it 2.312 r_scbond_other 2.312 r_mcbond_it 1.961 r_mcbond_other 1.92 r_angle_refined_deg 1.79 r_angle_other_deg 0.669 r_symmetry_nbd_other 0.199 r_nbd_refined 0.187 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.171 r_nbd_other 0.154 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_refined 0.066 r_ncsr_local_group_1 0.059 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5440 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 246
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing