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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with ibuprofenoyl-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 4.03 69.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 277.033 α = 90 b = 277.033 β = 90 c = 390.741 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) Rrim I (All) 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 2.17 226 100 0.276 0.282 0.053 0.998 10.4 27.7 393535
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 11.89 226 100 0.041 0.008 0.996 41.9 25.5
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 2.17 196.662 393489 19705 99.988 0.202 0.2005 0.209 0.239 0.2443 51.22
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] -0.159 -0.159 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.656 r_dihedral_angle_6_deg 14.275 r_lrange_other 9.9 r_lrange_it 9.885 r_dihedral_angle_2_deg 8.522 r_mcangle_other 7.545 r_mcangle_it 7.544 r_scangle_it 7.489 r_scangle_other 7.488 r_dihedral_angle_1_deg 7.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.656 r_dihedral_angle_6_deg 14.275 r_lrange_other 9.9 r_lrange_it 9.885 r_dihedral_angle_2_deg 8.522 r_mcangle_other 7.545 r_mcangle_it 7.544 r_scangle_it 7.489 r_scangle_other 7.488 r_dihedral_angle_1_deg 7.194 r_mcbond_it 5.019 r_mcbond_other 5.018 r_scbond_it 4.97 r_scbond_other 4.97 r_dihedral_angle_other_2_deg 2.792 r_angle_refined_deg 1.747 r_angle_other_deg 0.584 r_nbd_refined 0.223 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.157 r_nbd_other 0.138 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.088 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.06 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 32381 Nucleic Acid Atoms Solvent Atoms 1264 Heterogen Atoms 744
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building