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Crystal structure of dihydroorotate dehydrogenase from Leishmania donovani
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B4G PDB entry 2B4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 298 2.545M Sodium chloride, 0.1M Citric acid, 5mM Orotic acid pH 5.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.82 56.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.869 α = 90 b = 83.869 β = 90 c = 188.725 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 325 mm CCD 2007-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97950 SSRL BL9-2
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 1.8 50 100 0.098 9.1 5.2 137519
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 1.8 1.86 99.9 0.515 4.6 13796
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2B4G 1.8 33.88 137496 6902 99.96 0.168 0.166 0.1719 0.196 0.1992 RANDOM 18.249
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] 0.27 0.13 0.27 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.66 r_dihedral_angle_4_deg 14.246 r_dihedral_angle_3_deg 12.41 r_dihedral_angle_1_deg 6.16 r_scangle_it 3.652 r_scbond_it 2.258 r_angle_refined_deg 1.401 r_mcangle_it 1.371 r_angle_other_deg 0.949 r_mcbond_it 0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.66 r_dihedral_angle_4_deg 14.246 r_dihedral_angle_3_deg 12.41 r_dihedral_angle_1_deg 6.16 r_scangle_it 3.652 r_scbond_it 2.258 r_angle_refined_deg 1.401 r_mcangle_it 1.371 r_angle_other_deg 0.949 r_mcbond_it 0.751 r_mcbond_other 0.192 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9532 Nucleic Acid Atoms Solvent Atoms 752 Heterogen Atoms 212
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection