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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with ketoprofenoyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RMW
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 4.02 69.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.694 α = 90 b = 276.694 β = 90 c = 390.43 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 2024-04-25 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 2.08 225.751 100 0.302 0.059 0.996 7.9 27.3 444942
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 11.39 225.75 99.9 0.079 0.016 0.992 5.8 25.6
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 2.08 225.751 444853 22435 99.979 0.218 0.2161 0.2185 0.2507 0.254 46.779
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] -0.174 -0.174 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.67 r_dihedral_angle_2_deg 15.487 r_dihedral_angle_6_deg 14.428 r_lrange_other 8.769 r_lrange_it 8.765 r_dihedral_angle_1_deg 7.19 r_scangle_it 6.642 r_scangle_other 6.642 r_mcangle_it 6.546 r_mcangle_other 6.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.67 r_dihedral_angle_2_deg 15.487 r_dihedral_angle_6_deg 14.428 r_lrange_other 8.769 r_lrange_it 8.765 r_dihedral_angle_1_deg 7.19 r_scangle_it 6.642 r_scangle_other 6.642 r_mcangle_it 6.546 r_mcangle_other 6.546 r_scbond_it 4.41 r_scbond_other 4.41 r_mcbond_it 4.409 r_mcbond_other 4.409 r_dihedral_angle_other_2_deg 3.936 r_angle_refined_deg 1.798 r_angle_other_deg 0.584 r_nbd_refined 0.23 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.153 r_nbd_other 0.146 r_symmetry_nbd_refined 0.144 r_symmetry_xyhbond_nbd_other 0.086 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.08 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 32322 Nucleic Acid Atoms Solvent Atoms 1505 Heterogen Atoms 792
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building