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Beta-glucuronidase from Acidobacterium capsulatum in complex with inhibitor R3794
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VNY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.1 M LiSO4, 0.5 M AmSO4, 0.1 M Trissodium citrate
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.999 α = 90 b = 44.658 β = 97.46 c = 137.023 γ = 90
Symmetry Space Group I 1 2 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 EIGER X 16M 2022-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97 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 2 41.15 99.8 0.99 25.1 6.4 33997
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 2 2.05 100 0.99
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 41.15 32297 1698 99.75 0.19665 0.19419 0.2011 0.24406 0.2439 RANDOM 18.368
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] -0.76 0.64 2.1 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.38 r_dihedral_angle_4_deg 18.381 r_dihedral_angle_3_deg 14.849 r_dihedral_angle_1_deg 6.932 r_long_range_B_refined 4.751 r_long_range_B_other 4.461 r_scangle_other 2.446 r_mcangle_it 2.219 r_mcangle_other 2.218 r_scbond_it 1.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.38 r_dihedral_angle_4_deg 18.381 r_dihedral_angle_3_deg 14.849 r_dihedral_angle_1_deg 6.932 r_long_range_B_refined 4.751 r_long_range_B_other 4.461 r_scangle_other 2.446 r_mcangle_it 2.219 r_mcangle_other 2.218 r_scbond_it 1.675 r_scbond_other 1.617 r_angle_refined_deg 1.616 r_mcbond_it 1.5 r_mcbond_other 1.494 r_angle_other_deg 1.374 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3450 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing