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The structures of apo- and inhibitor bound human dihydroorotate dehydrogenase reveal conformational flexibility within the inhibitor binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 DROPS WERE FORMED BY MIXING EQUAL AMOUNTS OF 18-24 MG/ML PROTEIN IN
100 MM HEPES PH 7.0, 400 MM NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM
N,N- DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) WITH A PRECIPITANT SOLUTION
OF 0.1 M ACETATE PH 4.8 40 MM C11DAO, 20.8 MM
N,-DIMETHYLDECYLAMINE-N-OXIDE (DDAO), 2 MM DIHYDROOROTATE (DHO) THE
HANGING DROPS WERE INCUBATED AGAINST 0.5 ML RESERVOIR OF 0.1 M ACETATE
PH 4.8, 1.6-2.2 M AMMONIUM SULFATE AND 30% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.61 65.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.41 α = 90 b = 90.41 β = 90 c = 122.07 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2004-04-27 M SINGLE WAVELENGTH 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.092 MAX II I711
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 2.1 18.83 98 0.114 12.17 33570 -3 22.487
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 2.1 2.2 99.5 0.327 5.8 4367
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1d3g 2.1 18.83 31888 1678 0.16907 0.16771 0.1676 0.19441 0.1942 RANDOM 10.597
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] 0.16 0.08 0.16 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.984 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 5.696 r_scangle_it 2.081 r_angle_refined_deg 1.298 r_scbond_it 1.27 r_mcangle_it 0.755 r_mcbond_it 0.487 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.984 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 5.696 r_scangle_it 2.081 r_angle_refined_deg 1.298 r_scbond_it 1.27 r_mcangle_it 0.755 r_mcbond_it 0.487 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.191 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 2805 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement REFMAC refinement REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling CNS phasing