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Didydroorotate dehydrogenase from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DOR PDB entry 1dor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1M Sodium Tribasic Dihydrate pH 5.6, 1M Lithium Sulfate and 0.5M amonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.664 α = 90 b = 143.664 β = 90 c = 69.75 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 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18
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 2 124.035 99.95 0.071 0.064 10.5 5.6 55552 55526 1 2 20.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1dor 2 28.5 1 52702 52702 2820 100 0.17018 0.16866 0.1718 0.19962 0.2014 RANDOM 18.946
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] 0.38 0.19 0.38 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.814 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 12.601 r_dihedral_angle_1_deg 5.849 r_scangle_it 3.145 r_scbond_it 1.92 r_angle_refined_deg 1.202 r_mcangle_it 1.125 r_mcbond_it 0.728 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.814 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 12.601 r_dihedral_angle_1_deg 5.849 r_scangle_it 3.145 r_scbond_it 1.92 r_angle_refined_deg 1.202 r_mcangle_it 1.125 r_mcbond_it 0.728 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4584 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 74
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling