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Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 291 drops: 50mM HEPES, pH 7.7, 400mM NaCl, 30% glycerol, 1mM EDTA, 10mM N,N-dimethylundecylamin-N-oxide (C11DAO), precipitant solution: 0.1M acetate pH 4.6-5.0, 40mM C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM dihydroorotate (DHO), 1.8-2.4M ammonium sulfate, 1mM inhibitors, reservoir: 0.1M acetate pH 4.8, 2.4-2.6M ammonium sulfate, 30% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.68 66.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.888 α = 90 b = 90.888 β = 90 c = 122.915 γ = 120
Symmetry Space Group P 32 2 1
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 MARMOSAIC 225 mm CCD 2006-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 78.81 99.56 46965 46758 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.9 78.81 2 46758 42031 4727 99.56 0.18021 0.18021 0.17699 0.1759 0.20897 0.2086 RANDOM 18.73
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] 0.36 0.18 0.36 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.444 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 14.317 r_dihedral_angle_1_deg 5.653 r_scangle_it 3.772 r_scbond_it 2.339 r_mcangle_it 1.424 r_angle_refined_deg 1.413 r_mcbond_it 0.949 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.444 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 14.317 r_dihedral_angle_1_deg 5.653 r_scangle_it 3.772 r_scbond_it 2.339 r_mcangle_it 1.424 r_angle_refined_deg 1.413 r_mcbond_it 0.949 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.265 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 2781 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 71
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling