☰ Navigation Tabs
Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with glucuronic acid configured isofagamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PSH
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 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.046 α = 90 b = 44.669 β = 97.605 c = 137.173 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 EIGER2 X 16M 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 Diamond I04
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 1.25 42.44 99 0.998 10.2 6.2 136682
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 1.25 1.27 0.882
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 1.25 42.44 136675 6866 98.942 0.165 0.164 0.1675 0.184 0.1701 14.323
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] -0.448 0.55 1.049 -0.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.183 r_dihedral_angle_4_deg 18.799 r_dihedral_angle_3_deg 12.64 r_dihedral_angle_1_deg 6.291 r_lrange_it 5.114 r_lrange_other 5.093 r_scangle_it 3.985 r_scangle_other 3.984 r_scbond_it 2.692 r_scbond_other 2.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.183 r_dihedral_angle_4_deg 18.799 r_dihedral_angle_3_deg 12.64 r_dihedral_angle_1_deg 6.291 r_lrange_it 5.114 r_lrange_other 5.093 r_scangle_it 3.985 r_scangle_other 3.984 r_scbond_it 2.692 r_scbond_other 2.691 r_mcangle_it 2.222 r_mcangle_other 2.222 r_angle_refined_deg 1.931 r_angle_other_deg 1.642 r_mcbond_it 1.504 r_mcbond_other 1.498 r_chiral_restr_other 0.431 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.219 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.183 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.091 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3453 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing