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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with naproxenoyl-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 4.04 69.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.278 α = 90 b = 276.278 β = 90 c = 389.216 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 2 225.29 100 0.245 0.066 0.999 10.1 27.5 497035
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 10.95 225.29 100 0.039 0.008 1 39.6 26
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 2 225.29 496995 24747 99.992 0.208 0.2062 0.2142 0.239 0.2464 44.988
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] -0.349 -0.349 0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.798 r_dihedral_angle_6_deg 14.392 r_dihedral_angle_2_deg 12.079 r_lrange_other 8.961 r_lrange_it 8.954 r_dihedral_angle_1_deg 6.969 r_scangle_it 6.807 r_scangle_other 6.807 r_mcangle_it 6.175 r_mcangle_other 6.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.798 r_dihedral_angle_6_deg 14.392 r_dihedral_angle_2_deg 12.079 r_lrange_other 8.961 r_lrange_it 8.954 r_dihedral_angle_1_deg 6.969 r_scangle_it 6.807 r_scangle_other 6.807 r_mcangle_it 6.175 r_mcangle_other 6.175 r_dihedral_angle_other_2_deg 5.069 r_scbond_it 4.565 r_scbond_other 4.565 r_mcbond_it 4.3 r_mcbond_other 4.3 r_angle_refined_deg 1.861 r_angle_other_deg 0.593 r_nbd_refined 0.226 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.165 r_nbd_other 0.157 r_symmetry_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_other 0.092 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32568 Nucleic Acid Atoms Solvent Atoms 1793 Heterogen Atoms 768
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building