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Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (H126A 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, HANGING 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 2.73654652 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.106 α = 90 b = 79.153 β = 91.656 c = 59.103 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 2022-11-24 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 2.45 90.52 100 0.368 0.434 0.228 0.982 4.9 6.9 30851
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 2.45 2.55 3.093 3.731 2.066 0.278 6.1
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 2.45 90.515 30847 1468 99.981 0.191 0.1875 0.1909 0.2618 0.2693 48.129
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] 0.136 0.69 -2.912 2.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.325 r_dihedral_angle_6_deg 15.107 r_lrange_other 11.586 r_lrange_it 11.585 r_dihedral_angle_2_deg 10.575 r_scangle_it 10.244 r_scangle_other 10.242 r_mcangle_other 9.516 r_mcangle_it 9.515 r_dihedral_angle_1_deg 7.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.325 r_dihedral_angle_6_deg 15.107 r_lrange_other 11.586 r_lrange_it 11.585 r_dihedral_angle_2_deg 10.575 r_scangle_it 10.244 r_scangle_other 10.242 r_mcangle_other 9.516 r_mcangle_it 9.515 r_dihedral_angle_1_deg 7.955 r_scbond_it 7.828 r_scbond_other 7.826 r_mcbond_it 7.006 r_mcbond_other 6.994 r_angle_refined_deg 2.645 r_angle_other_deg 0.85 r_nbd_other 0.27 r_nbd_refined 0.239 r_symmetry_nbd_other 0.221 r_symmetry_nbd_refined 0.215 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.114 r_ncsr_local_group_1 0.114 r_symmetry_nbtor_other 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5356 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling Coot model building PHASER phasing