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Crystal structure of DHODH in complex with ferulenol from Eimeria tenella
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M HEPES, 1.8 M Triammonium citrate, 1 mM ferulenol
Crystal Properties Matthews coefficient Solvent content 3.03 59.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.984 α = 90 b = 132.984 β = 90 c = 214.998 γ = 120
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 RAYONIX MX300HE 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 3.65 50 96.1 0.075 7.9 4.3 24158
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 3.65 3.71 96.7 0.797 1.74 4.2
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 6AJ5 3.65 20 21056 1089 92.39 0.22508 0.22104 0.2235 0.30334 0.3021 RANDOM 61.906
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] -1.01 -0.51 -1.01 3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.894 r_dihedral_angle_3_deg 19.687 r_dihedral_angle_4_deg 14.845 r_dihedral_angle_1_deg 8.934 r_long_range_B_refined 4.033 r_long_range_B_other 4.032 r_mcangle_it 1.904 r_mcangle_other 1.904 r_angle_refined_deg 1.522 r_scangle_other 1.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.894 r_dihedral_angle_3_deg 19.687 r_dihedral_angle_4_deg 14.845 r_dihedral_angle_1_deg 8.934 r_long_range_B_refined 4.033 r_long_range_B_other 4.032 r_mcangle_it 1.904 r_mcangle_other 1.904 r_angle_refined_deg 1.522 r_scangle_other 1.373 r_mcbond_it 1.042 r_mcbond_other 1.041 r_angle_other_deg 1.03 r_scbond_it 0.697 r_scbond_other 0.697 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11764 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 276
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing