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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(3-(2-(3-Trifluoromethylphenyl)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 3.99 69.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.622 α = 90 b = 276.622 β = 90 c = 390.752 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 2024-04-25 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 2.25 225.774 100 0.291 0.056 0.997 9.7 27.7 352301
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 2.25 2.29 4.553 0.865 0.476 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 2.25 225.774 352056 17768 99.93 0.211 0.2091 0.2169 0.2506 0.2553 54.595
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] -1.666 -1.666 3.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.545 r_dihedral_angle_6_deg 14.351 r_dihedral_angle_2_deg 12.695 r_lrange_other 10.027 r_lrange_it 10.019 r_mcangle_it 7.681 r_mcangle_other 7.681 r_scangle_it 7.426 r_scangle_other 7.426 r_dihedral_angle_1_deg 7.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.545 r_dihedral_angle_6_deg 14.351 r_dihedral_angle_2_deg 12.695 r_lrange_other 10.027 r_lrange_it 10.019 r_mcangle_it 7.681 r_mcangle_other 7.681 r_scangle_it 7.426 r_scangle_other 7.426 r_dihedral_angle_1_deg 7.137 r_mcbond_it 5.048 r_mcbond_other 5.048 r_scbond_it 4.859 r_scbond_other 4.859 r_dihedral_angle_other_2_deg 2.466 r_angle_refined_deg 1.651 r_angle_other_deg 0.547 r_nbd_refined 0.224 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.163 r_nbd_other 0.146 r_symmetry_xyhbond_nbd_other 0.142 r_symmetry_nbd_refined 0.101 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_refined 0.056 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 32502 Nucleic Acid Atoms Solvent Atoms 839 Heterogen Atoms 864
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building