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Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-oxidized, ligand-free 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
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.122 α = 90 b = 146.844 β = 90 c = 66.18 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 PILATUS 2M 2015-06-29 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 1.8 50 99.7 0.07 37.4 6.13 125746
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 1.8 1.83 0.327
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 1.81 44.51 119239 6035 99.55 0.19945 0.19872 0.2065 0.21413 0.2232 RANDOM 20.761
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 10.836 r_dihedral_angle_1_deg 6.25 r_dihedral_angle_2_deg 2.477 r_long_range_B_refined 1.833 r_long_range_B_other 1.713 r_angle_refined_deg 0.918 r_mcangle_it 0.6 r_mcangle_other 0.6 r_scangle_other 0.526 r_angle_other_deg 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.836 r_dihedral_angle_1_deg 6.25 r_dihedral_angle_2_deg 2.477 r_long_range_B_refined 1.833 r_long_range_B_other 1.713 r_angle_refined_deg 0.918 r_mcangle_it 0.6 r_mcangle_other 0.6 r_scangle_other 0.526 r_angle_other_deg 0.346 r_mcbond_it 0.324 r_mcbond_other 0.324 r_scbond_it 0.291 r_scbond_other 0.291 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 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 9548 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 201
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing