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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(3-(3-Methoxybenzyloxy)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 3.96 68.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.277 α = 90 b = 276.277 β = 90 c = 388.791 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 2.2 225.21 100 0.314 0.061 0.997 9 27.7 373895
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 2.2 2.24 4.045 1.082 0.473
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 2.2 196.124 373792 18727 99.972 0.203 0.2016 0.2102 0.2395 0.2467 43.854
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] -0.626 -0.626 1.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.522 r_dihedral_angle_6_deg 14.904 r_dihedral_angle_2_deg 12.215 r_lrange_other 9.14 r_lrange_it 9.129 r_dihedral_angle_1_deg 7.126 r_mcangle_it 6.886 r_mcangle_other 6.886 r_scangle_it 6.643 r_scangle_other 6.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.522 r_dihedral_angle_6_deg 14.904 r_dihedral_angle_2_deg 12.215 r_lrange_other 9.14 r_lrange_it 9.129 r_dihedral_angle_1_deg 7.126 r_mcangle_it 6.886 r_mcangle_other 6.886 r_scangle_it 6.643 r_scangle_other 6.642 r_mcbond_it 4.517 r_mcbond_other 4.516 r_scbond_it 4.265 r_scbond_other 4.265 r_dihedral_angle_other_2_deg 3.43 r_angle_refined_deg 1.536 r_angle_other_deg 0.487 r_nbd_refined 0.224 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.182 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.069 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 32496 Nucleic Acid Atoms Solvent Atoms 1393 Heterogen Atoms 828
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building