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Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile
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 295 100 mM sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.071 α = 90 b = 143.071 β = 90 c = 68.997 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 MAR CCD 165 mm 2011-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.437 LNLS D03B-MX1
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 2.15 35.77 97.8 0.137 0.137 11.9 7 43015
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 2.15 2.27 98.1 0.803 0.803 2.6 6.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3GYE 2.15 35.77 43011 2164 97.852 0.18 0.1781 0.1785 0.2187 0.2197 26.369
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] -0.055 -0.028 -0.055 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.423 r_dihedral_angle_4_deg 16.64 r_dihedral_angle_3_deg 13.042 r_dihedral_angle_1_deg 7.394 r_lrange_it 3.964 r_lrange_other 3.928 r_scangle_it 2.763 r_scangle_other 2.762 r_mcangle_other 2.218 r_mcangle_it 2.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.423 r_dihedral_angle_4_deg 16.64 r_dihedral_angle_3_deg 13.042 r_dihedral_angle_1_deg 7.394 r_lrange_it 3.964 r_lrange_other 3.928 r_scangle_it 2.763 r_scangle_other 2.762 r_mcangle_other 2.218 r_mcangle_it 2.217 r_scbond_it 1.724 r_scbond_other 1.723 r_mcbond_it 1.421 r_mcbond_other 1.415 r_angle_refined_deg 1.314 r_angle_other_deg 1.273 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.188 r_symmetry_nbd_refined 0.174 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.167 r_nbd_other 0.153 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.061 r_bond_refined_d 0.006 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 4612 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing