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Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with serine
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 HEPES, 100 MM SODIUM CHLORIDE, 6% MPD
Crystal Properties Matthews coefficient Solvent content 3.33 63.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.157 α = 90 b = 122.157 β = 90 c = 128.184 γ = 120
Symmetry Space Group P 32 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 EIGER X 16M 2019-04-12 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) R Merge I (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 2.3 50 99.8 0.096 0.103 0.999 14.4 15.6 47207
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 2.3 2.44 99 0.763 0.876 2.7
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 2.3 19.99 46601 2489 99.67 0.17392 0.17196 0.1805 0.21019 0.2157 RANDOM 56.857
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_3_deg 16.583 r_dihedral_angle_4_deg 13.138 r_long_range_B_other 8.394 r_long_range_B_refined 8.393 r_scangle_other 6.822 r_dihedral_angle_1_deg 6.311 r_mcangle_it 4.575 r_mcangle_other 4.575 r_scbond_it 4.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_3_deg 16.583 r_dihedral_angle_4_deg 13.138 r_long_range_B_other 8.394 r_long_range_B_refined 8.393 r_scangle_other 6.822 r_dihedral_angle_1_deg 6.311 r_mcangle_it 4.575 r_mcangle_other 4.575 r_scbond_it 4.238 r_scbond_other 4.227 r_mcbond_it 3.157 r_mcbond_other 3.156 r_angle_refined_deg 1.445 r_angle_other_deg 0.974 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 5800 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing