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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(3-(2-Methylpropoxy)phenylthiol)propanoyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9I2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295.15 4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.99 69.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 277.268 α = 90 b = 277.268 β = 90 c = 388.969 γ = 90
Symmetry Space Group I 4 2 2
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 EIGER2 X 16M 2024-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953731 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.25 225.78 100 0.316 0.061 0.997 8.9 27.4 352323
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 4.659 0.941 0.58
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 2.25 195.244 352227 17549 99.971 0.221 0.219 0.2298 0.2536 0.2629 46.822
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] 0.293 0.293 -0.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.568 r_dihedral_angle_6_deg 14.346 r_dihedral_angle_2_deg 13.766 r_lrange_other 9.223 r_lrange_it 9.212 r_dihedral_angle_1_deg 7.162 r_scangle_it 6.849 r_scangle_other 6.849 r_mcangle_it 6.83 r_mcangle_other 6.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.568 r_dihedral_angle_6_deg 14.346 r_dihedral_angle_2_deg 13.766 r_lrange_other 9.223 r_lrange_it 9.212 r_dihedral_angle_1_deg 7.162 r_scangle_it 6.849 r_scangle_other 6.849 r_mcangle_it 6.83 r_mcangle_other 6.83 r_scbond_it 4.49 r_scbond_other 4.49 r_mcbond_it 4.479 r_mcbond_other 4.477 r_dihedral_angle_other_2_deg 2.868 r_angle_refined_deg 1.719 r_angle_other_deg 0.567 r_nbd_refined 0.224 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.18 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32545 Nucleic Acid Atoms Solvent Atoms 1016 Heterogen Atoms 768
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building