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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 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 2.74398351 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.053 α = 90 b = 79.09 β = 92.008 c = 59.194 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 1.65 90.471 100 0.091 0.108 0.057 0.999 8.9 6.8 100251
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 1.65 1.68 2.398 2.828 1.488 0.32 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 90.471 100247 5092 99.996 0.196 0.1944 0.1949 0.2251 0.2255 30.979
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] -0.349 0.299 -0.99 1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.581 r_dihedral_angle_3_deg 13.044 r_lrange_it 6.456 r_lrange_other 6.447 r_dihedral_angle_1_deg 6.33 r_dihedral_angle_2_deg 5.697 r_scangle_it 5.379 r_scangle_other 5.379 r_mcangle_it 3.827 r_mcangle_other 3.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.581 r_dihedral_angle_3_deg 13.044 r_lrange_it 6.456 r_lrange_other 6.447 r_dihedral_angle_1_deg 6.33 r_dihedral_angle_2_deg 5.697 r_scangle_it 5.379 r_scangle_other 5.379 r_mcangle_it 3.827 r_mcangle_other 3.827 r_scbond_it 3.567 r_scbond_other 3.567 r_mcbond_it 2.781 r_mcbond_other 2.781 r_angle_refined_deg 1.712 r_angle_other_deg 0.585 r_nbd_other 0.228 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.194 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.12 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5366 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling Coot model building PHASER phasing