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Crystal structure of human DHODH in complex with inhibitor 006
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 293.15 acetate, ammonium sulfate, glycerol, sodium chloride, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, ethylenediaminetetraacetic acid
Crystal Properties Matthews coefficient Solvent content 3.93 68.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.915 α = 90 b = 92.915 β = 90 c = 125.34 γ = 120
Symmetry Space Group P 32 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 293.15 PIXEL DECTRIS EIGER2 S 9M 2024-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0 SSRF BL19U1
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 1.9 80.4668 99.996 0.996 67.7 10.4 49715
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 5.16 0.183 0.041
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 28.98 1.38 49681 2010 99.83 0.201 0.2002 0.2012 0.2217 0.2233 26.62
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.4185 f_angle_d 0.9495 f_chiral_restr 0.0638 f_bond_d 0.0112 f_plane_restr 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2768 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing