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Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant Y142A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1M sodium citrate tribasic dihydrate pH 5.6, 1.1M lithium sulfate, 0.45M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.651 α = 90 b = 140.651 β = 90 c = 68.001 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 PIXEL DECTRIS PILATUS 2M 2016-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45868 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.75 121.807 100 0.109 0.116 0.04 11.2 7.8 77370
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 100 0.657 0.657 0.742 0.339 1.1 4.8
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 3GYE 1.75 121.807 73474 3856 99.98 0.1653 0.1641 0.1641 0.1883 0.1884 RANDOM 21.106
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 39.828 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_4_deg 12.371 r_dihedral_angle_1_deg 6.185 r_angle_refined_deg 1.503 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4604 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction