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Crystal structure of dihydroorotate dehydrogenase from Leishmania brasiliensis in complex with 5-(3-hydroxybenzylidene)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 294.15 1.4M ammonium sulfate, 0.75M lithium sulfate, 0.1M sodium citrate pH5.6
Crystal Properties Matthews coefficient Solvent content 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.575 α = 90 b = 104.895 β = 90 c = 106.742 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 PILATUS 2M 2023-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977180 LNLS SIRIUS MANACA
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 1.45 47.57 98.88 0.999 1.1 6.9 122018 24.41
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 1.45 1.46 0.521
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 1.45 47.57 1.34 122006 6100 98.88 0.1457 0.1444 0.1458 0.1711 0.1715 33.76
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 17.0292 f_angle_d 1.4301 f_chiral_restr 0.1237 f_bond_d 0.0122 f_plane_restr 0.0118
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4626 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing