7NEA

Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M3 mutant).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION293HEPES 0.1M pH 7.5; Sodium chloride 3.4M

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.497α = 90
b = 146.497β = 90
c = 143.776γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.7595.1398.60.0450.0550.030.99911.32.858749
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7898.20.8971.1020.6230.4012.8

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 REPLACEMENTTHROUGHOUT6GKR295.1337506199198.510.16340.16140.2007RANDOM31.195
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]
0.130.060.13-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.395
r_dihedral_angle_4_deg21.774
r_dihedral_angle_3_deg15.15
r_dihedral_angle_1_deg7.627
r_angle_refined_deg2.031
r_angle_other_deg1.533
r_chiral_restr0.113
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.395
r_dihedral_angle_4_deg21.774
r_dihedral_angle_3_deg15.15
r_dihedral_angle_1_deg7.627
r_angle_refined_deg2.031
r_angle_other_deg1.533
r_chiral_restr0.113
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2481
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms27

Software

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