8I04

Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with serine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7E3Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 MM HEPES, 100 MM SODIUM CHLORIDE, 6% MPD
Crystal Properties
Matthews coefficientSolvent content
3.3363.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.157α = 90
b = 122.157β = 90
c = 128.184γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35099.80.0960.1030.99914.415.647207
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)RedundancyNumber Unique Reflections (All)
12.32.44990.7630.8762.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7E3Y2.319.9946601248999.670.173920.171960.21019RANDOM56.857
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.387
r_dihedral_angle_3_deg16.583
r_dihedral_angle_4_deg13.138
r_long_range_B_other8.394
r_long_range_B_refined8.393
r_scangle_other6.822
r_dihedral_angle_1_deg6.311
r_mcangle_it4.575
r_mcangle_other4.575
r_scbond_it4.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.387
r_dihedral_angle_3_deg16.583
r_dihedral_angle_4_deg13.138
r_long_range_B_other8.394
r_long_range_B_refined8.393
r_scangle_other6.822
r_dihedral_angle_1_deg6.311
r_mcangle_it4.575
r_mcangle_other4.575
r_scbond_it4.238
r_scbond_other4.227
r_mcbond_it3.157
r_mcbond_other3.156
r_angle_refined_deg1.445
r_angle_other_deg0.974
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms5800
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing