6GKR

Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum in PLP-form (holo-form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GKP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION7.5293HEPES 0.1M pH 7.5; Sodium chloride 3.4M
Crystal Properties
Matthews coefficientSolvent content
2.0640.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.509α = 90
b = 146.61β = 90
c = 119.57γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.1984.0198.30.1720.9974.445692
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.192.26990.8840.6614.2

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 REPLACEMENTTHROUGHOUT6GKP2.1984.0143383230198.010.16170.15930.2058RANDOM30.27
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]
0.031.93-1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.888
r_dihedral_angle_4_deg18.996
r_dihedral_angle_3_deg15.162
r_dihedral_angle_1_deg7.235
r_angle_refined_deg1.604
r_chiral_restr0.113
r_bond_refined_d0.009
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7398
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms51

Software

Software
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling