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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with butanoyl-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 3.99 69.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.507 α = 90 b = 276.507 β = 90 c = 389.677 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 0.953738 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 2.02 225.504 100 0.282 0.055 0.999 11.1 27.4 483899
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 11.06 225.5 99.9 0.034 0.007 1 59 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.02 225.504 483840 24515 99.987 0.21 0.208 0.2434 0.2115 42.809
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] -0.004 -0.004 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.188 r_dihedral_angle_6_deg 15.268 r_dihedral_angle_2_deg 9.975 r_lrange_other 8.678 r_lrange_it 8.669 r_dihedral_angle_1_deg 7.036 r_scangle_it 6.774 r_scangle_other 6.773 r_mcangle_it 6.23 r_mcangle_other 6.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.188 r_dihedral_angle_6_deg 15.268 r_dihedral_angle_2_deg 9.975 r_lrange_other 8.678 r_lrange_it 8.669 r_dihedral_angle_1_deg 7.036 r_scangle_it 6.774 r_scangle_other 6.773 r_mcangle_it 6.23 r_mcangle_other 6.23 r_scbond_it 4.634 r_scbond_other 4.634 r_mcbond_it 4.241 r_mcbond_other 4.241 r_angle_refined_deg 1.646 r_dihedral_angle_other_2_deg 1.531 r_angle_other_deg 0.513 r_nbd_refined 0.225 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.157 r_nbd_other 0.154 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.074 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 32612 Nucleic Acid Atoms Solvent Atoms 1428 Heterogen Atoms 636
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building