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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-methyldecanoyl-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 4.04 69.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 277.034 α = 90 b = 277.034 β = 90 c = 390.861 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 2.11 226.02 100 0.267 0.052 0.996 10 27.4 427911
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 11.56 226.02 99.9 0.046 0.009 0.993 34.9 25.6
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 2.11 226.019 427679 21361 99.945 0.203 0.201 0.2078 0.239 0.2464 45.194
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] 0.009 0.009 -0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.33 r_dihedral_angle_6_deg 14.383 r_dihedral_angle_2_deg 8.571 r_lrange_other 8.485 r_lrange_it 8.483 r_dihedral_angle_1_deg 7.165 r_scangle_it 6.601 r_scangle_other 6.6 r_mcangle_other 6.382 r_mcangle_it 6.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.33 r_dihedral_angle_6_deg 14.383 r_dihedral_angle_2_deg 8.571 r_lrange_other 8.485 r_lrange_it 8.483 r_dihedral_angle_1_deg 7.165 r_scangle_it 6.601 r_scangle_other 6.6 r_mcangle_other 6.382 r_mcangle_it 6.381 r_scbond_other 4.403 r_scbond_it 4.402 r_mcbond_it 4.341 r_mcbond_other 4.341 r_dihedral_angle_other_2_deg 3.151 r_angle_refined_deg 1.838 r_angle_other_deg 0.596 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.134 r_nbd_other 0.127 r_symmetry_xyhbond_nbd_other 0.124 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.082 r_xyhbond_nbd_other 0.068 r_bond_refined_d 0.008 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 32536 Nucleic Acid Atoms Solvent Atoms 1668 Heterogen Atoms 720
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building