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Crystal structure of dihydroorotate dehydrogenase from Leishmania braziliensis in complex with 5-(4-hydroxy-3-methoxybenzyl)pyrimidine-2,4,6(1H,3H,5H)-trione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294.15 1.6M ammonium sulfate, 0.25M lithium sulfate, 0.1M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.31 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.72 α = 90 b = 105.47 β = 90 c = 106.12 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.85 47.6 99.98 0.999 12 7.1 59862 40.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.87 0.461 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 40.09 1.33 59848 5705 99.98 0.1756 0.1738 0.1791 0.2099 0.2181 50.83
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.6861 f_angle_d 0.9483 f_chiral_restr 0.0717 f_bond_d 0.0098 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4539 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 115
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing