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Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with Mannose-1-Phosphate
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 7 285
Crystal Properties Matthews coefficient Solvent content 2.36 47.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.534 α = 90 b = 83.368 β = 106.352 c = 73.206 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 2023-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979261 ALBA XALOC
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 2.1 48.7 96.7 0.085 7.1 3.4 40738
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 2.1 2.21 0.707
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 2.1 45.184 40716 2073 96.522 0.177 0.1754 0.1844 0.2093 0.2114 39.547
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] 0.772 -1.07 0.126 -0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.086 r_dihedral_angle_3_deg 11.526 r_dihedral_angle_1_deg 7.257 r_lrange_it 6.163 r_lrange_other 6.128 r_dihedral_angle_2_deg 5.197 r_scangle_it 3.594 r_scangle_other 3.594 r_mcangle_it 2.509 r_mcangle_other 2.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.086 r_dihedral_angle_3_deg 11.526 r_dihedral_angle_1_deg 7.257 r_lrange_it 6.163 r_lrange_other 6.128 r_dihedral_angle_2_deg 5.197 r_scangle_it 3.594 r_scangle_other 3.594 r_mcangle_it 2.509 r_mcangle_other 2.509 r_scbond_it 2.228 r_scbond_other 2.228 r_mcbond_it 1.647 r_mcbond_other 1.647 r_angle_refined_deg 1.312 r_angle_other_deg 0.46 r_symmetry_nbd_refined 0.211 r_nbd_other 0.197 r_symmetry_nbd_other 0.189 r_nbd_refined 0.184 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_other 0.111 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.077 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 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 5441 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing