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Structure of human D-glucuronyl C5 epimerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 21.5% P2K MME, 0.1 M Na cacodylate pH 6.0)
Crystal Properties Matthews coefficient Solvent content 3.2 61.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.82 α = 90 b = 99.82 β = 90 c = 262.97 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 PILATUS3 6M 2015-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.95373 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 2.52 43.83 99.5 0.11 12.2 5.7 47276 50.9
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 2.52 2.67 97.2 0.73 1.9 5.7
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 4PW2 2.52 43.83 47276 2489 99.5 0.178 0.176 0.1799 0.226 0.2288 RANDOM 54.66
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] -0.73 -0.37 -0.73 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.885 r_dihedral_angle_4_deg 16.936 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_1_deg 7.162 r_long_range_B_refined 6.675 r_long_range_B_other 6.675 r_scangle_other 4.837 r_mcangle_it 3.578 r_mcangle_other 3.578 r_scbond_it 2.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.885 r_dihedral_angle_4_deg 16.936 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_1_deg 7.162 r_long_range_B_refined 6.675 r_long_range_B_other 6.675 r_scangle_other 4.837 r_mcangle_it 3.578 r_mcangle_other 3.578 r_scbond_it 2.925 r_scbond_other 2.92 r_mcbond_it 2.172 r_mcbond_other 2.169 r_angle_refined_deg 1.583 r_angle_other_deg 0.961 r_chiral_restr 0.075 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 8291 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHENIX phasing