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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with decanoyl-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 69.18
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) 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 0.066 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) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 11.39 225.59 99.9 0.05 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-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 0.2018 0.2342 0.2009 39.638
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] -0.251 -0.251 0.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.103 r_dihedral_angle_6_deg 14.542 r_dihedral_angle_2_deg 9.009 r_lrange_it 8.187 r_lrange_other 8.182 r_dihedral_angle_1_deg 7.022 r_scangle_it 6.366 r_scangle_other 6.366 r_dihedral_angle_other_2_deg 5.844 r_mcangle_it 5.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.103 r_dihedral_angle_6_deg 14.542 r_dihedral_angle_2_deg 9.009 r_lrange_it 8.187 r_lrange_other 8.182 r_dihedral_angle_1_deg 7.022 r_scangle_it 6.366 r_scangle_other 6.366 r_dihedral_angle_other_2_deg 5.844 r_mcangle_it 5.725 r_mcangle_other 5.725 r_scbond_it 4.312 r_scbond_other 4.312 r_mcbond_it 3.8 r_mcbond_other 3.8 r_angle_refined_deg 1.874 r_angle_other_deg 0.596 r_nbd_refined 0.227 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.182 r_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.163 r_symmetry_nbd_refined 0.158 r_symmetry_xyhbond_nbd_other 0.12 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32457 Nucleic Acid Atoms Solvent Atoms 1692 Heterogen Atoms 708
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building