7K5A

The external aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A in complex with cesium ion at the metal coordination site.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K0B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829850 mM Bicine-CsOH, 9% PEG 8,000, 3 mM Spermine, pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.6152.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.827α = 90
b = 59.527β = 94.88
c = 67.478γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9720APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.591.08298.20.0820.0820.0950.0379.26.4113436
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5899.30.7150.7150.8350.32416.6

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 REPLACEMENTTHROUGHOUT7k0b1.539.29107437571397.840.17090.16830.22RANDOM30.771
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]
-1.230.461.050.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.53
r_dihedral_angle_4_deg18.998
r_dihedral_angle_3_deg12.82
r_dihedral_angle_1_deg6.223
r_rigid_bond_restr4.108
r_angle_refined_deg1.429
r_chiral_restr0.101
r_bond_refined_d0.008
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4897
Nucleic Acid Atoms
Solvent Atoms656
Heterogen Atoms80

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction