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The structures of human dihydroorotate dehydrogenase with inhibitor HL-008
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 293 300 mM NaCl, 50 mM HEPES, 1 mM EDTA, 22% glycerol, 10 mM UDAO and 20.8 mM DDAO, pH 7.7
Crystal Properties Matthews coefficient Solvent content 3.94 68.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.906 α = 90 b = 92.906 β = 90 c = 125.479 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 298.15 PIXEL STFC Large Pixel Detector 2024-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97946 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.86 30.41 98.7 0.134 0.041 0.996 4.4 19 2459728 22.07
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 1.86 5.05 0.975
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 1.86 30.41 1.35 52328 2491 98.3 0.2076 0.2067 0.206 0.226 0.2236
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 11.305 f_angle_d 1.106 f_chiral_restr 0.067 f_bond_d 0.011 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 80
Software Software Software Name Purpose MxCuBE data collection HKL-3000 data scaling PHENIX refinement