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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(3-(2-(3-Methoxyphenyl)ethoxy)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 3.98 69.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.667 α = 90 b = 276.667 β = 90 c = 389.559 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 2024-11-13 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 2 225.57 100 0.25 0.048 0.999 10.8 27.6 498887
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 4.601 0.929
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 2 195.541 498841 24859 99.991 0.209 0.2072 0.2169 0.2437 0.2525 44.935
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.715 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_6_deg 14.583 r_lrange_other 8.483 r_lrange_it 8.479 r_dihedral_angle_1_deg 7.08 r_scangle_it 6.471 r_scangle_other 6.471 r_mcangle_it 6.202 r_mcangle_other 6.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.715 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_6_deg 14.583 r_lrange_other 8.483 r_lrange_it 8.479 r_dihedral_angle_1_deg 7.08 r_scangle_it 6.471 r_scangle_other 6.471 r_mcangle_it 6.202 r_mcangle_other 6.202 r_scbond_it 4.289 r_scbond_other 4.289 r_mcbond_it 4.286 r_mcbond_other 4.286 r_dihedral_angle_other_2_deg 2.666 r_angle_refined_deg 1.742 r_angle_other_deg 0.576 r_nbd_refined 0.226 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.181 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.165 r_symmetry_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_other 0.125 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.079 r_bond_refined_d 0.008 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 32568 Nucleic Acid Atoms Solvent Atoms 1562 Heterogen Atoms 840
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building