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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis
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 3.98 69.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 275.45 α = 90 b = 275.45 β = 90 c = 388.331 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 2024-09-21 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 2.4 224.67 100 0.404 0.078 0.996 7.6 27.7 286594
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 13.15 224.67 100 0.062 0.063 0.017 0.999 23.6
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 2.4 224.67 286578 14384 99.994 0.214 0.2118 0.221 0.2504 0.2562 61.541
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] 0.1 0.1 -0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.613 r_dihedral_angle_6_deg 14.21 r_lrange_other 11.693 r_lrange_it 11.684 r_mcangle_other 9.43 r_mcangle_it 9.429 r_scangle_it 8.152 r_scangle_other 8.149 r_dihedral_angle_2_deg 7.871 r_dihedral_angle_1_deg 7.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.613 r_dihedral_angle_6_deg 14.21 r_lrange_other 11.693 r_lrange_it 11.684 r_mcangle_other 9.43 r_mcangle_it 9.429 r_scangle_it 8.152 r_scangle_other 8.149 r_dihedral_angle_2_deg 7.871 r_dihedral_angle_1_deg 7.478 r_mcbond_it 6.153 r_mcbond_other 6.15 r_scbond_it 5.24 r_scbond_other 5.238 r_angle_refined_deg 1.629 r_angle_other_deg 0.556 r_nbd_refined 0.236 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.174 r_nbd_other 0.119 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.077 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_refined 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32200 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building