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Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TV5 PDB ENTRY 1TV5
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, EVAPORATION, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.16 61.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.858 α = 90 b = 85.858 β = 90 c = 138.352 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 2008-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.00 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 50 91.5 0.058 45 12 45761 42194 1.9 1.9
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 2.06 68 0.515 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1TV5 2 50 1.5 41320 37754 802 91.37 0.2126 0.2122 0.2122 0.2217 0.24807 0.2444 RANDOM 45.511
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] 1.22 0.61 1.22 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.658 r_dihedral_angle_4_deg 21.719 r_dihedral_angle_3_deg 15.24 r_dihedral_angle_1_deg 6.367 r_scangle_it 2.728 r_scbond_it 1.747 r_mcangle_it 1.383 r_angle_refined_deg 1.308 r_mcbond_it 0.816 r_symmetry_vdw_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.658 r_dihedral_angle_4_deg 21.719 r_dihedral_angle_3_deg 15.24 r_dihedral_angle_1_deg 6.367 r_scangle_it 2.728 r_scbond_it 1.747 r_mcangle_it 1.383 r_angle_refined_deg 1.308 r_mcbond_it 0.816 r_symmetry_vdw_refined 0.322 r_nbtor_refined 0.309 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2934 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 79
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling