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The structure of a beta-glucuronidase from glycoside hydrolase family 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Sodium Bromide, 0.1M BIS-TRIS pH 7.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.929 α = 90 b = 67.17 β = 95.93 c = 96.72 γ = 90
Symmetry Space Group C 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 2018-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 2.43 96.2 99.5 0.064 11.3 10 37999 19.57
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 2.43 2.52 99.3 0.161 5.8 9.5
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 (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 5dmy 2.43 96.2 36036 1961 99.52 0.16704 0.16464 0.1646 0.21149 0.212 RANDOM 25.334
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] 2.56 1.3 -1.21 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.44 r_dihedral_angle_4_deg 19.741 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 6.655 r_long_range_B_refined 3.963 r_long_range_B_other 3.758 r_angle_other_deg 3.632 r_scangle_other 2.321 r_mcangle_it 2.172 r_mcangle_other 2.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.44 r_dihedral_angle_4_deg 19.741 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 6.655 r_long_range_B_refined 3.963 r_long_range_B_other 3.758 r_angle_other_deg 3.632 r_scangle_other 2.321 r_mcangle_it 2.172 r_mcangle_other 2.171 r_scbond_it 1.454 r_scbond_other 1.454 r_mcbond_it 1.288 r_mcbond_other 1.288 r_angle_refined_deg 1.162 r_chiral_restr 0.044 r_bond_refined_d 0.008 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d 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 7575 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing