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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with acetyl-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 = 276.626 α = 90 b = 276.626 β = 90 c = 390.302 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 1.88 225.69 100 0.209 0.04 0.999 11.5 27.5 600791
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 10.3 225.69 99.9 0.033 0.007 1 59.2 26.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.88 225.689 600724 30182 99.988 0.205 0.2035 0.2342 0.2133 38.82
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] 0.027 0.027 -0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.229 r_dihedral_angle_6_deg 15.447 r_dihedral_angle_2_deg 12.503 r_lrange_it 7.734 r_lrange_other 7.733 r_dihedral_angle_1_deg 6.945 r_scangle_it 6.186 r_scangle_other 6.186 r_mcangle_it 5.579 r_mcangle_other 5.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.229 r_dihedral_angle_6_deg 15.447 r_dihedral_angle_2_deg 12.503 r_lrange_it 7.734 r_lrange_other 7.733 r_dihedral_angle_1_deg 6.945 r_scangle_it 6.186 r_scangle_other 6.186 r_mcangle_it 5.579 r_mcangle_other 5.579 r_scbond_it 4.272 r_scbond_other 4.272 r_mcbond_it 4.07 r_mcbond_other 4.07 r_angle_refined_deg 1.618 r_dihedral_angle_other_2_deg 0.95 r_angle_other_deg 0.516 r_nbd_refined 0.223 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.161 r_nbd_other 0.148 r_symmetry_xyhbond_nbd_other 0.135 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.009 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 32572 Nucleic Acid Atoms Solvent Atoms 1894 Heterogen Atoms 612
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building