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Leishmania major Dihydroorotate Dehydrogenase in complex with orotate
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, HANGING DROP 5.6 293 1.2M lithium sulfate, 0.3M ammonium sulfate in 0.1 M sodium citrate tribasic dihydrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.167 α = 90 b = 142.167 β = 90 c = 69.157 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 2006-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.43800 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 1.9 30 99.9 0.077 0.069 9.3 4.8 62830 62830 1 1 22.86
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) 1.9 2 99.6 0.537 0.475 3.4 4.7 9144
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 3gye 1.9 30 1 1 59615 59615 3185 99.9 0.17813 0.17673 0.1758 0.20419 0.2042 RANDOM 21.313
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] 0.42 0.21 0.42 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.596 r_dihedral_angle_4_deg 13.635 r_dihedral_angle_3_deg 11.918 r_dihedral_angle_1_deg 5.994 r_scangle_it 2.662 r_scbond_it 1.665 r_angle_refined_deg 1.182 r_mcangle_it 1.003 r_mcbond_it 0.634 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.596 r_dihedral_angle_4_deg 13.635 r_dihedral_angle_3_deg 11.918 r_dihedral_angle_1_deg 5.994 r_scangle_it 2.662 r_scbond_it 1.665 r_angle_refined_deg 1.182 r_mcangle_it 1.003 r_mcbond_it 0.634 r_nbtor_refined 0.307 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4554 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 108
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling