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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,
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 3.62 65.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.05 α = 90 b = 90.05 β = 90 c = 123.2 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 3 19.5 99.5 0.25 6.85 11941 -3 18.753
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) 3 4 100 0.346 5 6817
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 3 19.5 11938 597 100 0.193 0.19 0.1891 0.253 0.252 RANDOM 17.718
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] 0.69 0.34 0.69 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.969 r_dihedral_angle_3_deg 19.459 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_1_deg 6.748 r_scangle_it 3.533 r_scbond_it 2.065 r_angle_refined_deg 1.787 r_mcangle_it 1.367 r_mcbond_it 0.79 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.969 r_dihedral_angle_3_deg 19.459 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_1_deg 6.748 r_scangle_it 3.533 r_scbond_it 2.065 r_angle_refined_deg 1.787 r_mcangle_it 1.367 r_mcbond_it 0.79 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2805 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 42
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction CNS phasing