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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(4-(2-Phenylethoxy)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 69.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.859 α = 90 b = 276.859 β = 90 c = 389.854 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 2024-09-20 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 2.3 225.73 100 0.377 0.073 0.996 8.5 27.7 329823
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 2.3 2.34 4.73 0.897 0.423 0.8
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 2.3 138.814 329689 16780 99.959 0.203 0.201 0.2101 0.2437 0.2506 48.94
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] -1.07 -1.07 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.308 r_dihedral_angle_6_deg 14.237 r_dihedral_angle_2_deg 10.778 r_lrange_other 9.334 r_lrange_it 9.326 r_dihedral_angle_1_deg 7.16 r_mcangle_it 6.961 r_mcangle_other 6.961 r_scangle_it 6.681 r_scangle_other 6.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.308 r_dihedral_angle_6_deg 14.237 r_dihedral_angle_2_deg 10.778 r_lrange_other 9.334 r_lrange_it 9.326 r_dihedral_angle_1_deg 7.16 r_mcangle_it 6.961 r_mcangle_other 6.961 r_scangle_it 6.681 r_scangle_other 6.68 r_mcbond_it 4.498 r_mcbond_other 4.498 r_scbond_it 4.279 r_scbond_other 4.278 r_dihedral_angle_other_2_deg 2.312 r_angle_refined_deg 1.635 r_angle_other_deg 0.543 r_nbd_refined 0.223 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.181 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.077 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32572 Nucleic Acid Atoms Solvent Atoms 1297 Heterogen Atoms 816
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building