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Dihydroorotate Dehydrogenase (DHODH) crystal structure in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3G pdb entry 1D3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.8 293 ammonium sulfate, pH 4.8, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.41 63.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.028 α = 90 b = 91.028 β = 90 c = 122.465 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 2006-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.90005 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.18 48.34 99.8 0.142 31139 26.3
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 2.18 2.27 99.5 0.516
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 pdb entry 1D3G 2.18 48.34 31139 1557 99.86 0.1611 0.1588 0.1658 0.2049 0.2115 RANDOM 28.9191
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] 0.7 0.35 0.7 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.465 r_dihedral_angle_4_deg 18.769 r_dihedral_angle_3_deg 15.04 r_scangle_it 7.447 r_dihedral_angle_1_deg 5.914 r_scbond_it 5.651 r_mcangle_it 3.42 r_mcbond_it 3.104 r_angle_refined_deg 1.437 r_angle_other_deg 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.465 r_dihedral_angle_4_deg 18.769 r_dihedral_angle_3_deg 15.04 r_scangle_it 7.447 r_dihedral_angle_1_deg 5.914 r_scbond_it 5.651 r_mcangle_it 3.42 r_mcbond_it 3.104 r_angle_refined_deg 1.437 r_angle_other_deg 0.921 r_mcbond_other 0.745 r_symmetry_vdw_other 0.302 r_nbd_refined 0.209 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.14 r_nbtor_other 0.088 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling