☰ Navigation Tabs
Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with 1,2-beta-mannobiose
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 4.76 74.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.183 α = 90 b = 178.183 β = 90 c = 83.675 γ = 120
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 0.97926 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 2.65 154.31 100 0.076 7.1 5.7 44200
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 2.65 2.79 0.752
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.65 50 44174 2184 99.937 0.17 0.1689 0.1816 0.2 71.379
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] -3.916 -3.916 7.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.006 r_dihedral_angle_6_deg 8.43 r_dihedral_angle_1_deg 5.833 r_lrange_it 5.095 r_lrange_other 5.095 r_mcangle_it 3.312 r_mcangle_other 3.311 r_scangle_it 3.007 r_scangle_other 3.007 r_mcbond_it 1.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.006 r_dihedral_angle_6_deg 8.43 r_dihedral_angle_1_deg 5.833 r_lrange_it 5.095 r_lrange_other 5.095 r_mcangle_it 3.312 r_mcangle_other 3.311 r_scangle_it 3.007 r_scangle_other 3.007 r_mcbond_it 1.898 r_mcbond_other 1.898 r_dihedral_angle_2_deg 1.87 r_scbond_it 1.679 r_scbond_other 1.679 r_angle_refined_deg 0.732 r_angle_other_deg 0.289 r_symmetry_nbd_refined 0.18 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.17 r_nbd_refined 0.148 r_nbd_other 0.128 r_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_refined 0.05 r_ncsr_local_group_1 0.037 r_chiral_restr 0.032 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5466 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing