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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with flurbiprofenoyl-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 4.06 69.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.476 α = 90 b = 276.476 β = 90 c = 391.895 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 2.2 225.914 100 0.407 0.079 0.994 7.1 27.3 377344
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 12.05 225.91 99.8 0.058 0.012 0.99 21.1 25.2
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 2.2 225.914 377256 19315 99.976 0.212 0.2106 0.2197 0.2453 0.2531 46.445
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] 0.057 0.057 -0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.018 r_dihedral_angle_3_deg 15.916 r_dihedral_angle_6_deg 14.494 r_lrange_other 9.794 r_lrange_it 9.782 r_dihedral_angle_1_deg 7.244 r_scangle_it 7.212 r_scangle_other 7.212 r_mcangle_it 7.112 r_mcangle_other 7.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.018 r_dihedral_angle_3_deg 15.916 r_dihedral_angle_6_deg 14.494 r_lrange_other 9.794 r_lrange_it 9.782 r_dihedral_angle_1_deg 7.244 r_scangle_it 7.212 r_scangle_other 7.212 r_mcangle_it 7.112 r_mcangle_other 7.112 r_scbond_it 4.664 r_scbond_other 4.664 r_mcbond_it 4.638 r_mcbond_other 4.638 r_dihedral_angle_other_2_deg 2.623 r_angle_refined_deg 1.806 r_angle_other_deg 0.592 r_nbd_refined 0.225 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.182 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.113 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.081 r_symmetry_nbd_refined 0.081 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.008 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 32491 Nucleic Acid Atoms Solvent Atoms 1167 Heterogen Atoms 780
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building