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Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM2
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 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.917 α = 90 b = 85.917 β = 90 c = 138.697 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 2009-02-23 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 2.4 50 99.8 0.053 41.8 7.3 29340 29285 2.2 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) 2.4 2.48 100 0.51 4 7.5 1465
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 3I65 2.4 50 4 29285 27709 1477 99.53 0.224 0.214 0.214 0.2316 0.267 0.2666 RANDOM 63.445
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] 1.79 0.89 1.79 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.226 r_dihedral_angle_4_deg 15.727 r_dihedral_angle_3_deg 14.809 r_dihedral_angle_1_deg 5.703 r_scangle_it 2.083 r_scbond_it 1.337 r_angle_refined_deg 1.251 r_mcangle_it 1.2 r_mcbond_it 0.681 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.226 r_dihedral_angle_4_deg 15.727 r_dihedral_angle_3_deg 14.809 r_dihedral_angle_1_deg 5.703 r_scangle_it 2.083 r_scbond_it 1.337 r_angle_refined_deg 1.251 r_mcangle_it 1.2 r_mcbond_it 0.681 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.088 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2999 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 67
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling