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Crystal structure of the full-length dihydroorotate dehydrogenase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold P9WHL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 0,2 M Sodium Chloride, 0,1 M Tris-HCl pH 8,5 and 25 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.05 α = 90 b = 85.215 β = 90 c = 181.005 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2022-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 3.8 41.508 97.5 0.253 0.279 0.988 5 5.5 39498 116.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 4 1.229 1.358 0.688 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.8 41.508 7194 354 95.869 0.259 0.2551 0.2572 0.3278 0.3307 125.462
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] -1.45 16.102 -14.653
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.768 r_lrange_other 27.768 r_mcangle_it 16.315 r_mcangle_other 16.314 r_scangle_it 15.707 r_scangle_other 15.705 r_dihedral_angle_3_deg 13.637 r_dihedral_angle_6_deg 11.238 r_mcbond_it 9.83 r_mcbond_other 9.83
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.768 r_lrange_other 27.768 r_mcangle_it 16.315 r_mcangle_other 16.314 r_scangle_it 15.707 r_scangle_other 15.705 r_dihedral_angle_3_deg 13.637 r_dihedral_angle_6_deg 11.238 r_mcbond_it 9.83 r_mcbond_other 9.83 r_scbond_it 9.232 r_scbond_other 9.23 r_dihedral_angle_1_deg 5.356 r_dihedral_angle_2_deg 2.976 r_angle_refined_deg 0.974 r_angle_other_deg 0.343 r_symmetry_xyhbond_nbd_refined 0.271 r_nbd_other 0.26 r_symmetry_nbd_refined 0.244 r_symmetry_nbd_other 0.212 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.172 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.073 r_chiral_restr 0.049 r_chiral_restr_other 0.013 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5192 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing