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Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with Phenyl isothiocyanate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GYE PDB ENTRY 3GYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE pH 5.6, 1.3M LITHIUM SULFATE, 0.3M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.75 55.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.19 α = 90 b = 144.19 β = 90 c = 69.87 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 MARMOSAIC 225 mm CCD 2011-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.461 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.56 22.43 99.9 0.077 0.077 18.2 8.8 116828 116828 2.5 17.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.65 99.9 0.218 0.218 7.8 7.8 16994
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3GYE 1.56 22.43 110920 110920 5843 99.84 0.17726 0.17639 0.1748 0.19352 0.1915 RANDOM 17.43
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 r_dihedral_angle_2_deg 40.094 r_dihedral_angle_4_deg 14.545 r_dihedral_angle_3_deg 11.247 r_dihedral_angle_1_deg 5.878 r_angle_refined_deg 1.275 r_chiral_restr 0.085 r_gen_planes_refined 0.007 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4731 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 114
Software Software Software Name Purpose NatXray data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling