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Crystal structure of beta-glucuronidase from Acidobacterium capsulatum at 1.24 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.5 M AmSO4
1 M LiSO4
0.1 M Trisodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.43 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.865 α = 90 b = 44.149 β = 97.577 c = 136.277 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 PILATUS 6M-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.911880 Diamond I04-1
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 1.24 74.69 97.2 0.998 11.6 6.1 134306
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 1.26 1.26 0.794 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5g0m 1.24 74.69 134258 6827 96.845 0.17 0.1686 0.1766 0.1878 0.1936 16.347
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] -0.922 0.17 0.688 0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.547 r_dihedral_angle_4_deg 17.424 r_dihedral_angle_3_deg 12.174 r_dihedral_angle_1_deg 6.315 r_lrange_it 4.923 r_lrange_other 4.85 r_scangle_it 3.763 r_scangle_other 3.762 r_scbond_it 2.563 r_scbond_other 2.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.547 r_dihedral_angle_4_deg 17.424 r_dihedral_angle_3_deg 12.174 r_dihedral_angle_1_deg 6.315 r_lrange_it 4.923 r_lrange_other 4.85 r_scangle_it 3.763 r_scangle_other 3.762 r_scbond_it 2.563 r_scbond_other 2.562 r_angle_other_deg 2.405 r_mcangle_it 2.289 r_mcangle_other 2.289 r_angle_refined_deg 1.959 r_mcbond_it 1.6 r_mcbond_other 1.6 r_nbd_refined 0.232 r_symmetry_nbd_other 0.221 r_nbd_other 0.217 r_symmetry_xyhbond_nbd_refined 0.212 r_nbtor_refined 0.191 r_symmetry_nbd_refined 0.163 r_symmetry_xyhbond_nbd_other 0.121 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.083 r_bond_other_d 0.036 r_gen_planes_other 0.02 r_bond_refined_d 0.018 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3372 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing