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Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-reduced, fumarate-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 1.3 M malonate, 0.2 M citrate, 0.1 M fumarate (co-crytallization). soaked into saturated sodium fumarate (15-30min), and then saturated dithionite (< 1min)
Crystal Properties Matthews coefficient Solvent content 2.33 47.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.854 α = 90 b = 146.604 β = 90 c = 64.9 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 CCD ADSC QUANTUM 270 2018-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.48 50 100 0.13 23.5 7.16 46000
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 2.48 2.54 0.555
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 2.48 42.98 43628 2231 99.02 0.16607 0.16298 0.1706 0.22774 0.2264 RANDOM 33.007
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.87 r_dihedral_angle_1_deg 6.687 r_dihedral_angle_2_deg 5.472 r_long_range_B_refined 5.157 r_long_range_B_other 5.154 r_scangle_other 3.943 r_mcangle_it 2.741 r_mcangle_other 2.741 r_scbond_it 2.421 r_scbond_other 2.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.87 r_dihedral_angle_1_deg 6.687 r_dihedral_angle_2_deg 5.472 r_long_range_B_refined 5.157 r_long_range_B_other 5.154 r_scangle_other 3.943 r_mcangle_it 2.741 r_mcangle_other 2.741 r_scbond_it 2.421 r_scbond_other 2.419 r_mcbond_it 1.794 r_mcbond_other 1.794 r_angle_refined_deg 1.333 r_angle_other_deg 0.56 r_chiral_restr 0.093 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 9548 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 233
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing