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Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-reduced, 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 1.6 M malonate, 48 mM citrate. soaked into 50 mM L-dihydroorotate (15 min), and then saturated dithionite (< 1min)
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.052 α = 90 b = 146.329 β = 90 c = 65.619 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 1.0800 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 2 50 99.2 0.094 16.94 10.57 91110
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 2.03 0.846
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 2 50 86554 4556 99.82 0.17598 0.17433 0.1841 0.20747 0.2125 RANDOM 29.493
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 12.82 r_dihedral_angle_1_deg 6.194 r_dihedral_angle_2_deg 4.635 r_long_range_B_refined 3.895 r_long_range_B_other 3.88 r_scangle_other 2.785 r_mcangle_it 2.016 r_mcangle_other 2.016 r_scbond_it 1.637 r_scbond_other 1.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.82 r_dihedral_angle_1_deg 6.194 r_dihedral_angle_2_deg 4.635 r_long_range_B_refined 3.895 r_long_range_B_other 3.88 r_scangle_other 2.785 r_mcangle_it 2.016 r_mcangle_other 2.016 r_scbond_it 1.637 r_scbond_other 1.636 r_angle_refined_deg 1.241 r_mcbond_it 1.23 r_mcbond_other 1.228 r_angle_other_deg 0.463 r_chiral_restr 0.063 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 311 Heterogen Atoms 245
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing