☰ Navigation Tabs
Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-oxidized, dihydroorotate-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 1.5 M malonate, 0.1 M citrate, 10 mM L-dihydroorotate. soaked into 50 mM L-dihydroorotate (15 min).
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.12 α = 90 b = 146.655 β = 90 c = 66.287 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 4M 2020-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0000 Photon Factory BL-1A
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 1.9 50 99.9 0.104 16.33 6.7 108205
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 1.9 1.93 0.731
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 5XFV 1.9 49.17 102832 5413 99.95 0.18378 0.18282 0.1912 0.20165 0.209 RANDOM 23.795
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.718 r_dihedral_angle_1_deg 6.4 r_dihedral_angle_2_deg 3.019 r_long_range_B_refined 2.306 r_long_range_B_other 2.169 r_angle_refined_deg 1.025 r_mcangle_it 0.93 r_mcangle_other 0.93 r_scangle_other 0.911 r_mcbond_it 0.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.718 r_dihedral_angle_1_deg 6.4 r_dihedral_angle_2_deg 3.019 r_long_range_B_refined 2.306 r_long_range_B_other 2.169 r_angle_refined_deg 1.025 r_mcangle_it 0.93 r_mcangle_other 0.93 r_scangle_other 0.911 r_mcbond_it 0.511 r_mcbond_other 0.511 r_scbond_it 0.508 r_scbond_other 0.508 r_angle_other_deg 0.4 r_chiral_restr 0.054 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 9573 Nucleic Acid Atoms Solvent Atoms 683 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing