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Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3H Homo sapiens DHODH, PDB ID: 1D3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 277 ammonium sulfate, sodium acetate, C8E5, dihydroorotic acid, A77 1726, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.95 58.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.428 α = 90 b = 105.428 β = 90 c = 276.632 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 4 2002-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9474 CHESS A1
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 2.4 50 98 0.074 8.6 4.7 23068 23068 32.6
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) 1 2.4 2.52 99.8 0.324 2.3 4.7 3376
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 Homo sapiens DHODH, PDB ID: 1D3H 2.4 33.48 2 22925 21786 1139 97.3 0.208 0.2011 0.201 0.1976 0.243 0.1961 RANDOM 35.7
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] 3.78 2.74 3.78 -7.56
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 3.38 c_mcangle_it 2.35 c_scbond_it 2.24 c_mcbond_it 1.42 c_angle_deg 1.4 c_improper_angle_d 0.77 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2944 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 114
Software Software Software Name Purpose DENZO data reduction SCALA data scaling RESOLVE model building CNS refinement CCP4 data scaling RESOLVE phasing