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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(4-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 3.99 69.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 277.431 α = 90 b = 277.431 β = 90 c = 388.43 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 2.15 225.76 100 0.278 0.054 0.998 9.4 27.7 403283
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 4.267 0.469 0.8 28.5
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 2.15 225.76 403252 20057 99.991 0.22 0.2185 0.2284 0.2564 0.2651 47.082
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] -0.317 -0.317 0.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.525 r_dihedral_angle_6_deg 14.42 r_dihedral_angle_2_deg 10.296 r_lrange_other 9.308 r_lrange_it 9.298 r_dihedral_angle_1_deg 7 r_mcangle_it 6.993 r_mcangle_other 6.993 r_scangle_it 6.858 r_scangle_other 6.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.525 r_dihedral_angle_6_deg 14.42 r_dihedral_angle_2_deg 10.296 r_lrange_other 9.308 r_lrange_it 9.298 r_dihedral_angle_1_deg 7 r_mcangle_it 6.993 r_mcangle_other 6.993 r_scangle_it 6.858 r_scangle_other 6.858 r_mcbond_it 4.583 r_mcbond_other 4.582 r_scbond_it 4.445 r_scbond_other 4.445 r_dihedral_angle_other_2_deg 2.279 r_angle_refined_deg 1.684 r_angle_other_deg 0.567 r_symmetry_xyhbond_nbd_refined 0.228 r_nbd_refined 0.223 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.156 r_nbd_other 0.147 r_symmetry_nbd_refined 0.133 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.082 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 32480 Nucleic Acid Atoms Solvent Atoms 1050 Heterogen Atoms 804
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building