☰ Navigation Tabs
Crystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-oxidized, 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 1.0 M malonate, 0.1 M citrate. soaked into saturated sodium fumarate (15-30min)
Crystal Properties Matthews coefficient Solvent content 2.43 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.627 α = 90 b = 146.529 β = 90 c = 65.488 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 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.98 50 95.8 0.098 22 4.03 92469
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 0.361
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 1.98 30.15 83992 4530 94.06 0.18049 0.17863 0.1872 0.21475 0.2214 RANDOM 26.054
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.228 r_dihedral_angle_1_deg 5.972 r_long_range_B_refined 4.428 r_long_range_B_other 4.397 r_dihedral_angle_2_deg 4.223 r_scangle_other 3.378 r_mcangle_it 2.218 r_mcangle_other 2.218 r_scbond_it 2.071 r_scbond_other 2.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.228 r_dihedral_angle_1_deg 5.972 r_long_range_B_refined 4.428 r_long_range_B_other 4.397 r_dihedral_angle_2_deg 4.223 r_scangle_other 3.378 r_mcangle_it 2.218 r_mcangle_other 2.218 r_scbond_it 2.071 r_scbond_other 2.069 r_mcbond_it 1.436 r_mcbond_other 1.435 r_angle_refined_deg 1.25 r_angle_other_deg 0.482 r_chiral_restr 0.063 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.005 r_bond_other_d 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 9558 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing