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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(4-(2-(3-Methoxyphenyl)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 4.01 69.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 277.169 α = 90 b = 277.169 β = 90 c = 391.174 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 2024-02-08 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 2.2 226.15 100 0.06 0.997 10.8 27.4 378534
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 1.001 0.351
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 2.2 196.355 378481 18924 99.987 0.211 0.2089 0.217 0.2484 0.2535 46.386
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] -0.025 -0.025 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.004 r_dihedral_angle_6_deg 15.021 r_dihedral_angle_2_deg 13.65 r_lrange_other 9.381 r_lrange_it 9.369 r_dihedral_angle_1_deg 7.184 r_mcangle_it 7.027 r_mcangle_other 7.027 r_scangle_it 7.025 r_scangle_other 7.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.004 r_dihedral_angle_6_deg 15.021 r_dihedral_angle_2_deg 13.65 r_lrange_other 9.381 r_lrange_it 9.369 r_dihedral_angle_1_deg 7.184 r_mcangle_it 7.027 r_mcangle_other 7.027 r_scangle_it 7.025 r_scangle_other 7.025 r_mcbond_it 4.595 r_mcbond_other 4.595 r_scbond_other 4.555 r_scbond_it 4.554 r_dihedral_angle_other_2_deg 2.317 r_angle_refined_deg 1.53 r_angle_other_deg 0.483 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.195 r_nbd_other 0.184 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.176 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_other 0.141 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 32439 Nucleic Acid Atoms Solvent Atoms 1099 Heterogen Atoms 840
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building