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Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3H PDB ID 1D3H
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 3.7 66.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.013 α = 90 b = 91.013 β = 90 c = 123.207 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 1.8 26.82 99.3 55038 54653 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.847 93.48
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 1D3H 1.8 26.82 2 49666 48931 5474 98.52 0.17897 0.17897 0.17622 0.20362 0.19 RANDOM 19.515
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] 0.03 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.929 r_dihedral_angle_4_deg 15.573 r_dihedral_angle_3_deg 13.092 r_dihedral_angle_1_deg 5.678 r_scangle_it 3.429 r_scbond_it 2.166 r_angle_refined_deg 1.347 r_mcangle_it 1.314 r_mcbond_it 0.865 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.929 r_dihedral_angle_4_deg 15.573 r_dihedral_angle_3_deg 13.092 r_dihedral_angle_1_deg 5.678 r_scangle_it 3.429 r_scbond_it 2.166 r_angle_refined_deg 1.347 r_mcangle_it 1.314 r_mcbond_it 0.865 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.244 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2790 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 78
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling