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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with isobutanoyl-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 4.01 69.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.488 α = 90 b = 276.488 β = 90 c = 390.12 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 1.94 225.58 100 0.237 0.046 0.999 12.5 27.4 546383
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 10.63 225.58 100 0.033 0.006 1 61.8 26.1
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 1.94 225.579 546282 27491 99.98 0.209 0.2071 0.2176 0.2384 0.2483 36.588
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] 0.153 0.153 -0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.315 r_dihedral_angle_6_deg 15.57 r_dihedral_angle_2_deg 12.768 r_lrange_it 8.242 r_lrange_other 8.234 r_dihedral_angle_1_deg 6.903 r_scangle_it 6.305 r_scangle_other 6.304 r_mcangle_it 5.707 r_mcangle_other 5.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.315 r_dihedral_angle_6_deg 15.57 r_dihedral_angle_2_deg 12.768 r_lrange_it 8.242 r_lrange_other 8.234 r_dihedral_angle_1_deg 6.903 r_scangle_it 6.305 r_scangle_other 6.304 r_mcangle_it 5.707 r_mcangle_other 5.707 r_scbond_it 4.316 r_scbond_other 4.316 r_mcbond_it 3.965 r_mcbond_other 3.964 r_angle_refined_deg 1.655 r_angle_other_deg 0.523 r_nbd_refined 0.223 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.176 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.151 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.077 r_xyhbond_nbd_other 0.049 r_dihedral_angle_other_2_deg 0.017 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 32587 Nucleic Acid Atoms Solvent Atoms 2055 Heterogen Atoms 636
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building