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Structure of human D-glucuronyl C5 epimerase in complex with product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HZZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Na acetate pH 5.5, 24% MPEG 5K and 0.1 M MES pH 6.5, 1.25 M lithium acetate
Crystal Properties Matthews coefficient Solvent content 3.11 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.811 α = 90 b = 99.811 β = 90 c = 260.488 γ = 120
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 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97914 SOLEIL PROXIMA 1
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 2.45 49.06 100 0.14 17.4 14.3 51003 41.6
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 2.45 2.5 100 1.63 1.6
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 6HZZ 2.45 49.06 51003 2671 99.9 0.175 0.173 0.1789 0.218 0.225 RANDOM 54.73
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] 0.02 0.01 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_3_deg 17.027 r_dihedral_angle_4_deg 16.764 r_dihedral_angle_1_deg 7.379 r_long_range_B_refined 6.732 r_long_range_B_other 6.732 r_scangle_other 4.888 r_mcangle_it 3.176 r_mcangle_other 3.176 r_scbond_it 3.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_3_deg 17.027 r_dihedral_angle_4_deg 16.764 r_dihedral_angle_1_deg 7.379 r_long_range_B_refined 6.732 r_long_range_B_other 6.732 r_scangle_other 4.888 r_mcangle_it 3.176 r_mcangle_other 3.176 r_scbond_it 3.114 r_scbond_other 3.112 r_mcbond_it 1.979 r_mcbond_other 1.978 r_angle_refined_deg 1.683 r_angle_other_deg 0.978 r_chiral_restr 0.079 r_bond_refined_d 0.012 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 8289 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 569
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing