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Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with Mannose
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, SITTING DROP 285 0.2 M Calcium acetate, 0.1 M Imidazole pH 8.0, 20 %PEG 1000
Crystal Properties Matthews coefficient Solvent content 4.8 74.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.629 α = 90 b = 176.629 β = 90 c = 83.539 γ = 120
Symmetry Space Group P 61 2 2
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 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.55 47.586 100 0.102 4.8 40.3 1030781
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.69 0.718
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 2.55 47.586 25524 1278 99.969 0.181 0.1795 0.1871 0.2067 0.2078 59.848
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] 0.041 0.021 0.041 -0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.744 r_dihedral_angle_3_deg 13.441 r_lrange_other 9.575 r_lrange_it 9.56 r_dihedral_angle_1_deg 7.675 r_scangle_it 7.558 r_scangle_other 7.556 r_mcangle_it 6.45 r_mcangle_other 6.449 r_dihedral_angle_2_deg 6.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.744 r_dihedral_angle_3_deg 13.441 r_lrange_other 9.575 r_lrange_it 9.56 r_dihedral_angle_1_deg 7.675 r_scangle_it 7.558 r_scangle_other 7.556 r_mcangle_it 6.45 r_mcangle_other 6.449 r_dihedral_angle_2_deg 6.089 r_scbond_it 4.936 r_scbond_other 4.934 r_mcbond_it 4.54 r_mcbond_other 4.537 r_angle_refined_deg 1.392 r_angle_other_deg 0.48 r_symmetry_nbd_other 0.191 r_nbd_refined 0.185 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.154 r_nbd_other 0.131 r_symmetry_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.085 r_symmetry_nbd_refined 0.084 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.032 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2733 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing