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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with octanoyl-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 69.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.305 α = 90 b = 276.305 β = 90 c = 390.677 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 0.953731 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 2.08 225.59 100 0.341 0.347 0.066 0.997 9.2 27.5 443965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 11.37 225.59 99.9 0.05 0.051 0.01 0.998 40.3 25.8
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 2.08 225.587 443883 22339 99.981 0.203 0.2012 0.2119 0.2331 0.2407 39.596
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] -0.254 -0.254 0.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.359 r_dihedral_angle_6_deg 14.483 r_dihedral_angle_2_deg 11.053 r_lrange_it 8.158 r_lrange_other 8.157 r_dihedral_angle_1_deg 7.035 r_dihedral_angle_other_2_deg 6.916 r_scangle_it 6.338 r_scangle_other 6.338 r_mcangle_it 5.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.359 r_dihedral_angle_6_deg 14.483 r_dihedral_angle_2_deg 11.053 r_lrange_it 8.158 r_lrange_other 8.157 r_dihedral_angle_1_deg 7.035 r_dihedral_angle_other_2_deg 6.916 r_scangle_it 6.338 r_scangle_other 6.338 r_mcangle_it 5.751 r_mcangle_other 5.751 r_scbond_it 4.274 r_scbond_other 4.274 r_mcbond_it 3.812 r_mcbond_other 3.812 r_angle_refined_deg 1.864 r_angle_other_deg 0.597 r_nbd_refined 0.225 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.182 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_other 0.058 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 32512 Nucleic Acid Atoms Solvent Atoms 1764 Heterogen Atoms 684
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building