7TCS

M379A mutant tyrosine phenol-lyase complexed with L-methionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VLH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES, pH 7.5, 0.2 mM PLP, 1 mM EDTA, 1 mM DTT, 19% PEG 5000 MME, 0.4 M CsCl
Crystal Properties
Matthews coefficientSolvent content
2.1342.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.55α = 93.73
b = 82.99β = 105.71
c = 96.58γ = 114.24
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.353.8787.10.99810.467.836383320.01
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3460.274

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2VLH1.3745.271.96335283200193.980.14130.14120.154928.1
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.8405
f_angle_d0.9047
f_chiral_restr0.0699
f_plane_restr0.0086
f_bond_d0.0059
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14451
Nucleic Acid Atoms
Solvent Atoms1682
Heterogen Atoms107

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing