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Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-oxidized, orotate-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 1.2 M malonate, 0.1 M citrate (8.3), 100 mM Arg, 12.5 mM OA (co-crystallization).
Crystal Properties Matthews coefficient Solvent content 2.45 49.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.687 α = 90 b = 146.531 β = 90 c = 65.986 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 315 2016-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.4 50 99.9 0.14 18.8 7.13 53983
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 2.4 2.44 0.493
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 2.4 46.15 51287 2640 99.67 0.18545 0.18313 0.1904 0.22997 0.2355 RANDOM 29.739
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] -0.05 0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.548 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 4.685 r_long_range_B_other 4.685 r_scangle_other 3.469 r_mcangle_it 2.376 r_mcangle_other 2.376 r_scbond_it 2.07 r_scbond_other 2.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.548 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 4.685 r_long_range_B_other 4.685 r_scangle_other 3.469 r_mcangle_it 2.376 r_mcangle_other 2.376 r_scbond_it 2.07 r_scbond_other 2.067 r_mcbond_it 1.477 r_mcbond_other 1.476 r_angle_refined_deg 1.252 r_angle_other_deg 0.469 r_chiral_restr 0.062 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 9402 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing