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Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7E3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 MM Potassium sodium tartrate, 5 MM DTT, 5 MM cysteine, 100 MM CoA
Crystal Properties Matthews coefficient Solvent content 2.91 57.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.71 α = 90 b = 161.71 β = 90 c = 161.71 γ = 90
Symmetry Space Group I 21 3
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 EIGER X 16M 2019-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 99.9 0.102 1 26 30.4 24563
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 99.8 1.319 0.861 2.8 29.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7E3Y 2.5 19.91 23224 1280 99.72 0.19248 0.19034 0.2002 0.23167 0.2366 RANDOM 77.536
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.482 r_dihedral_angle_3_deg 17.032 r_dihedral_angle_4_deg 14.797 r_long_range_B_refined 10.159 r_long_range_B_other 10.159 r_scangle_other 8.154 r_mcangle_other 7.28 r_mcangle_it 7.279 r_dihedral_angle_1_deg 6.816 r_scbond_it 5.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.482 r_dihedral_angle_3_deg 17.032 r_dihedral_angle_4_deg 14.797 r_long_range_B_refined 10.159 r_long_range_B_other 10.159 r_scangle_other 8.154 r_mcangle_other 7.28 r_mcangle_it 7.279 r_dihedral_angle_1_deg 6.816 r_scbond_it 5.58 r_scbond_other 5.578 r_mcbond_it 5.199 r_mcbond_other 5.194 r_angle_refined_deg 1.714 r_angle_other_deg 1.035 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3633 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing