3R4T

Crystal structure of 4-aminobutyrate aminotransferase GabT from Mycobacterium marinum covalently bound to pyridoxal phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OKS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289MymaA.01026.b.A1 PW29968 at 27.8 mg/mL against JCSG+ screen condition D5, 70% MPD, 0.1 M Hepes pH 7.5, crystal tracking ID 220563d5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.4964.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.62α = 90
b = 123.62β = 90
c = 157.59γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97946ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.5501000.11815.338.92625325245-337.813
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.571000.5593.749.11834

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 REPLACEMENTTHROUGHOUT3oks2.55025110128199.460.15330.15130.191RANDOM28.8302
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]
0.940.470.94-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.899
r_dihedral_angle_3_deg14.095
r_dihedral_angle_4_deg12.841
r_dihedral_angle_1_deg6.106
r_scangle_it3.874
r_scbond_it2.267
r_angle_refined_deg1.453
r_mcangle_it1.107
r_mcbond_it0.541
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.899
r_dihedral_angle_3_deg14.095
r_dihedral_angle_4_deg12.841
r_dihedral_angle_1_deg6.106
r_scangle_it3.874
r_scbond_it2.267
r_angle_refined_deg1.453
r_mcangle_it1.107
r_mcbond_it0.541
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3293
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms13

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
XDSdata reduction