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Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM74
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I65 PDB ENTRY 3I65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.16 M Ammonium sulfate, 0.1 M Sodium Acetate, pH 4.6, 18-20% PEG4000, 25% Glycerol, and 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.13 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.442 α = 90 b = 85.442 β = 90 c = 138.554 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 high-resolution double-crystal monochromator 2009-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 50 99.9 0.063 32.5 7.5 20143 19853 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.75 100 0.624 3.4 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3I65 2.5 50 19000 18778 1013 99.88 0.23849 0.23648 0.2448 0.27595 0.2831 RANDOM 72.691
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] 1.91 0.96 1.91 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.476 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 5.392 r_scangle_it 1.191 r_angle_refined_deg 1.072 r_mcangle_it 0.801 r_scbond_it 0.723 r_mcbond_it 0.444 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.476 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 5.392 r_scangle_it 1.191 r_angle_refined_deg 1.072 r_mcangle_it 0.801 r_scbond_it 0.723 r_mcbond_it 0.444 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.094 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2984 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 63
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling