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R. hominis 2 beta-glucuronidase bound to UNC10201652-glucuronide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.17 M Ammonium Acetate, 0.085M Sodium Citrate:HCl, pH 5.6 and 25.5 % (w/v) PEG 4000, 15 % (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3 58.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.414 α = 90 b = 145.95 β = 90 c = 281.383 γ = 90
Symmetry Space Group P 2 21 21
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 2021-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 2.7 49.96 99.3 0.07723 0.1092 0.07723 0.994 7.37 2 113475 56.08
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 2.7 2.8 99.5 0.7643 1.081 0.7643 0.559 1.13 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 49.96 1.34 113414 2000 99.34 0.2323 0.2314 0.2329 0.2825 0.2832 64.83
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.9468 f_angle_d 0.7589 f_chiral_restr 0.0518 f_plane_restr 0.0035 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20494 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 299
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing