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Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 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 293K
Crystal Properties Matthews coefficient Solvent content 3.66 66.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.696 α = 90 b = 90.696 β = 90 c = 122.95 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 2006-04-25 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) R Merge 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 30.74 100 0.088 14.3 5.6 40134 40134 2 2 14.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.238 6.1 5.6 5807
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1D3H 2 29.69 38083 36072 2011 99.96 0.17947 0.17839 0.1787 0.19937 0.2007 RANDOM 5.209
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] 0.29 0.15 0.29 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.623 r_dihedral_angle_4_deg 18.647 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 5.229 r_scangle_it 1.823 r_angle_refined_deg 1.085 r_scbond_it 1.081 r_mcangle_it 0.394 r_nbtor_refined 0.298 r_symmetry_hbond_refined 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.623 r_dihedral_angle_4_deg 18.647 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 5.229 r_scangle_it 1.823 r_angle_refined_deg 1.085 r_scbond_it 1.081 r_mcangle_it 0.394 r_nbtor_refined 0.298 r_symmetry_hbond_refined 0.278 r_mcbond_it 0.257 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2758 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 76
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling