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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(4-(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 3.98 69.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 277.189 α = 90 b = 277.189 β = 90 c = 388.554 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) 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 2.2 225.65 100 0.062 0.997 9.7 27.6 376085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 0.825 0.391
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 2.2 195.035 375924 18826 99.956 0.204 0.2022 0.2114 0.2377 0.2453 44.008
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] 0.214 0.214 -0.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.458 r_dihedral_angle_6_deg 14.418 r_dihedral_angle_2_deg 10.877 r_lrange_other 8.746 r_lrange_it 8.735 r_dihedral_angle_1_deg 7.03 r_mcangle_it 6.559 r_mcangle_other 6.559 r_scangle_it 6.491 r_scangle_other 6.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.458 r_dihedral_angle_6_deg 14.418 r_dihedral_angle_2_deg 10.877 r_lrange_other 8.746 r_lrange_it 8.735 r_dihedral_angle_1_deg 7.03 r_mcangle_it 6.559 r_mcangle_other 6.559 r_scangle_it 6.491 r_scangle_other 6.491 r_dihedral_angle_other_2_deg 4.921 r_mcbond_it 4.293 r_mcbond_other 4.293 r_scbond_it 4.23 r_scbond_other 4.23 r_angle_refined_deg 1.726 r_angle_other_deg 0.572 r_nbd_refined 0.223 r_symmetry_nbd_other 0.196 r_nbd_other 0.187 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.164 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.112 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 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 32548 Nucleic Acid Atoms Solvent Atoms 1118 Heterogen Atoms 768
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building