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Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol
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 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.195 α = 90 b = 142.195 β = 90 c = 68.735 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 2011-02-28 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 1.8 35.24 100 0.085 0.085 14.8 6.4 73441
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 1.8 1.9 98.8 0.704 0.704 2.5 6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3GYE 1.8 35.24 73409 3702 99.969 0.164 0.1627 0.163 0.1844 0.1839 5.04 20.497
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] -0.02 -0.01 -0.02 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.914 r_dihedral_angle_4_deg 14.539 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_1_deg 7.061 r_lrange_it 3.939 r_lrange_other 3.88 r_scangle_it 2.465 r_scangle_other 2.465 r_mcangle_other 1.684 r_mcangle_it 1.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.914 r_dihedral_angle_4_deg 14.539 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_1_deg 7.061 r_lrange_it 3.939 r_lrange_other 3.88 r_scangle_it 2.465 r_scangle_other 2.465 r_mcangle_other 1.684 r_mcangle_it 1.683 r_scbond_it 1.588 r_scbond_other 1.587 r_angle_other_deg 1.37 r_angle_refined_deg 1.309 r_mcbond_it 1.084 r_mcbond_other 1.076 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.17 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.147 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4626 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing