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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (E241A mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.15 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 0.1 M sodium HEPES-MOPS, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.71437407 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.619 α = 90 b = 78.989 β = 92.191 c = 58.923 γ = 90
Symmetry Space Group C 1 2 1
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 2022-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.85 90.244 100 0.128 0.152 0.081 0.998 8.2 6.8 70688
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 1.85 1.89 1.823 2.156 1.142 0.5 6.9
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 1.85 90.244 70667 3590 99.967 0.195 0.193 0.2363 0.2235 31.274
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] 0.083 0.418 -2.186 2.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.034 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_2_deg 8.764 r_lrange_it 8.013 r_lrange_other 7.994 r_dihedral_angle_1_deg 7.207 r_scangle_it 6.86 r_scangle_other 6.859 r_mcangle_it 5.385 r_mcangle_other 5.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.034 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_2_deg 8.764 r_lrange_it 8.013 r_lrange_other 7.994 r_dihedral_angle_1_deg 7.207 r_scangle_it 6.86 r_scangle_other 6.859 r_mcangle_it 5.385 r_mcangle_other 5.385 r_scbond_it 5.012 r_scbond_other 5.011 r_mcbond_it 4.152 r_mcbond_other 4.152 r_angle_refined_deg 2.323 r_angle_other_deg 0.803 r_nbd_other 0.261 r_nbd_refined 0.244 r_symmetry_xyhbond_nbd_refined 0.222 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.189 r_symmetry_nbd_refined 0.186 r_xyhbond_nbd_refined 0.181 r_symmetry_xyhbond_nbd_other 0.132 r_chiral_restr 0.118 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5358 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling Coot model building PHASER phasing