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Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.16 M Ammonium sulfate, 12-13% PEG4000, 0.1 M Sodium Acetate, pH 4.8, and 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.21 61.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.471 α = 90 b = 85.471 β = 90 c = 138.275 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 ADSC QUANTUM 315 2012-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.07 50 98.9 0.047 39.8 7.1 36975 36567 2.3 2.3 41.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.1 99 0.831 2.3 7.1 1809
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.07 28 2.3 36928 34734 1832 99.01 0.1858 0.18851 0.18578 0.23967 0.2441 RANDOM 54.339
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] 1.11 0.55 1.11 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.176 r_dihedral_angle_4_deg 17.705 r_dihedral_angle_3_deg 17.585 r_dihedral_angle_1_deg 7.398 r_angle_refined_deg 2.242 r_chiral_restr 0.165 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.176 r_dihedral_angle_4_deg 17.705 r_dihedral_angle_3_deg 17.585 r_dihedral_angle_1_deg 7.398 r_angle_refined_deg 2.242 r_chiral_restr 0.165 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2974 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 85
Software Software Software Name Purpose HKL-3000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling