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Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM959 (6-cyclopropyl-2,4-dimethyl-3-((6-(trifluoromethyl)pyridin-3-yl)methyl)-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 1.6 M Ammonium sulfate, 0.1 M Citric Acid pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.23 61.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.224 α = 90 b = 85.224 β = 90 c = 139.888 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 CCD MARMOSAIC 325 mm CCD 2020-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 2.9 50 99 0.97 10.06 10.3 12638
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 2.9 2.95 0.463 1.01
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 3.1 40.76 1.34 9320 955 88.94 0.1976 0.1936 0.1973 0.2283 0.2227 60.59
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 15.8359 f_angle_d 0.5086 f_chiral_restr 0.0416 f_plane_restr 0.0043 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2962 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing