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Bacteroides salyersiae GH164 beta-mannosidase in complex with mannoimidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T5O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 ammonium tartrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.71 α = 92.29 b = 104.743 β = 97.273 c = 170.568 γ = 106.301
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 X 16M 2019-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976230 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 168.66 100 0.998 6.9 2 424506
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 1.8 1.83 0.666
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 6t5o 1.8 168.66 424505 21073 99.96 0.208 0.2065 0.2065 0.2312 0.2311 39.475
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] 2.236 1.593 0.199 0.068 0.686 -3.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_4_deg 18.975 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_1_deg 7.219 r_lrange_it 6.999 r_lrange_other 6.99 r_scangle_it 5.821 r_scangle_other 5.821 r_mcangle_it 4.384 r_mcangle_other 4.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_4_deg 18.975 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_1_deg 7.219 r_lrange_it 6.999 r_lrange_other 6.99 r_scangle_it 5.821 r_scangle_other 5.821 r_mcangle_it 4.384 r_mcangle_other 4.384 r_scbond_it 4.005 r_scbond_other 4.005 r_mcbond_it 3.343 r_mcbond_other 3.342 r_angle_other_deg 2.31 r_angle_refined_deg 1.427 r_nbd_other 0.273 r_symmetry_nbd_refined 0.255 r_symmetry_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.203 r_nbd_refined 0.2 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.071 r_symmetry_nbtor_other 0.068 r_bond_other_d 0.035 r_symmetry_xyhbond_nbd_other 0.02 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31572 Nucleic Acid Atoms Solvent Atoms 1666 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing