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Crystal structure of human Dihydroorotate Dehydrogenase in complex with the inhibitor N-(3'-(2,2-difluoropropoxy)-2,3,5,6-tetrafluoro-[1,1'-biphenyl]-4-yl)-2-hydroxypyrazolo[1,5-a]pyridine-3-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 2 M ammonium sulphate, 100 mM sodium acetate pH 4.8 and 20 % v/v glycerol
Crystal Properties Matthews coefficient Solvent content 3.47 64.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.071 α = 90 b = 91.071 β = 90 c = 123.441 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 83.15 PIXEL DECTRIS PILATUS3 6M 2021-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 48.61 98.6 0.24 0.978 2 5.8 18434
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 2.6 2.74 0.661
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 2.6 41.15 1.34 18387 921 98.29 0.1792 0.1764 0.1802 0.2325 0.2321
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 10.346 f_angle_d 1.229 f_chiral_restr 0.063 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2892 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement SCALA data scaling XDS data reduction PHASER phasing