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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (D156A 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,
Crystal Properties Matthews coefficient Solvent content 2.70480084 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.473 α = 90 b = 78.745 β = 92.151 c = 58.943 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 XE 16M 2023-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 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 1.64 90.173 99 0.093 0.11 0.058 0.998 9.9 6.9 99692
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 1.64 1.67 2.09 2.456 1.283 0.372 7.1
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 1.64 90.173 99684 5055 98.828 0.18 0.1787 0.1799 0.2108 0.2137 27.835
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] 0.302 0.034 -0.718 0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.053 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_2_deg 12.36 r_lrange_it 6.778 r_lrange_other 6.759 r_dihedral_angle_1_deg 6.481 r_scangle_it 6.243 r_scangle_other 6.242 r_scbond_it 4.494 r_scbond_other 4.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.053 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_2_deg 12.36 r_lrange_it 6.778 r_lrange_other 6.759 r_dihedral_angle_1_deg 6.481 r_scangle_it 6.243 r_scangle_other 6.242 r_scbond_it 4.494 r_scbond_other 4.494 r_mcangle_it 4.181 r_mcangle_other 4.181 r_mcbond_other 3.379 r_mcbond_it 3.378 r_angle_refined_deg 2.113 r_angle_other_deg 0.759 r_nbd_other 0.328 r_symmetry_xyhbond_nbd_refined 0.244 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.215 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.121 r_symmetry_nbtor_other 0.086 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 5360 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling Coot model building PHASER phasing