5F9S

Crystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.7 Angstrom; internal aldimine with PLP in the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HOC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5294Protein solution; 0.2 M AGT, 18mM potassium phosphate pH7.4, 20mM Hepes pH 7.4, 5% Jeffamine (Hampton), 5mM sodium hydroxylamine. Reservoir; PEG 6k 12%, 100 mM MES pH 5.0. Mixing: 1+1 microL Cryoprotectant; 25% MPD
Crystal Properties
Matthews coefficientSolvent content
2.1442.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.479α = 90
b = 101.88β = 90
c = 131.338γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.00ELETTRA5.2R

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
11.748.04870.0820.0420.99710.64.27007020.08
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7383.40.6140.3240.7551.63.93510

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-VALUE1hoc1.745.1181.3470010341186.270.16050.15830.204722.7206
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_d14.617
f_angle_d1.15
f_chiral_restr0.056
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5977
Nucleic Acid Atoms
Solvent Atoms802
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata reduction