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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(3-Benzyloxyphenylthio)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 4.04 69.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.13 α = 90 b = 276.13 β = 90 c = 392.062 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 2024-07-25 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 2 225.76 100 0.266 0.052 0.998 10.3 27.4 500145
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 10.95 225.76 0.069 0.014 0.996 36.9
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 2 196.019 500045 25132 99.979 0.218 0.2164 0.2273 0.25 0.2589 42.367
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] -0.306 -0.306 0.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.458 r_dihedral_angle_6_deg 14.627 r_dihedral_angle_2_deg 12.134 r_lrange_other 8.333 r_lrange_it 8.329 r_dihedral_angle_1_deg 7.224 r_scangle_it 6.232 r_scangle_other 6.232 r_mcangle_it 6.136 r_mcangle_other 6.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.458 r_dihedral_angle_6_deg 14.627 r_dihedral_angle_2_deg 12.134 r_lrange_other 8.333 r_lrange_it 8.329 r_dihedral_angle_1_deg 7.224 r_scangle_it 6.232 r_scangle_other 6.232 r_mcangle_it 6.136 r_mcangle_other 6.136 r_dihedral_angle_other_2_deg 5.807 r_mcbond_it 4.199 r_mcbond_other 4.199 r_scbond_it 4.12 r_scbond_other 4.12 r_angle_refined_deg 1.834 r_angle_other_deg 0.602 r_nbd_refined 0.227 r_symmetry_nbd_other 0.196 r_nbd_other 0.195 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.17 r_symmetry_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.125 r_symmetry_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32439 Nucleic Acid Atoms Solvent Atoms 1306 Heterogen Atoms 804
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building