☰ Navigation Tabs
Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(4-(3-Methoxybenzyloxy)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 69.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.85 α = 90 b = 276.85 β = 90 c = 390.049 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 2024-09-20 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 2.3 225.76 100 0.348 0.067 0.996 7.3 27.5 329974
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 2.3 2.34 5.549 0.368
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 2.3 196.532 329796 16805 99.946 0.2 0.1979 0.2066 0.2425 0.2481 54.02
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] -0.467 -0.467 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.424 r_dihedral_angle_6_deg 14.188 r_dihedral_angle_2_deg 12.063 r_lrange_other 10.037 r_lrange_it 10.025 r_mcangle_it 7.526 r_mcangle_other 7.526 r_scangle_it 7.526 r_scangle_other 7.526 r_dihedral_angle_1_deg 7.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.424 r_dihedral_angle_6_deg 14.188 r_dihedral_angle_2_deg 12.063 r_lrange_other 10.037 r_lrange_it 10.025 r_mcangle_it 7.526 r_mcangle_other 7.526 r_scangle_it 7.526 r_scangle_other 7.526 r_dihedral_angle_1_deg 7.136 r_mcbond_it 4.947 r_mcbond_other 4.946 r_scbond_it 4.898 r_scbond_other 4.898 r_dihedral_angle_other_2_deg 3.162 r_angle_refined_deg 1.649 r_angle_other_deg 0.545 r_nbd_refined 0.226 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.152 r_nbd_other 0.146 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_nbtor_other 0.082 r_symmetry_nbd_refined 0.078 r_chiral_restr 0.074 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 32455 Nucleic Acid Atoms Solvent Atoms 1141 Heterogen Atoms 828
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building