6Q8E

Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum in PMP-form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5288Ammonium acetate 0.2M; MES 0.1M pH 6.0; PEG 3350 25%

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.75α = 90
b = 144.75β = 90
c = 144.5γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.9677ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.519.8399.90.0620.0670.99917.047.4719239826.282
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.699.80.6990.7490.8292.837.711

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 REPLACEMENTTHROUGHOUT6GKR1.519.8387783459599.840.14180.13990.1763RANDOM22.829
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]
0.690.350.69-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.971
r_dihedral_angle_4_deg18.422
r_dihedral_angle_3_deg14.982
r_dihedral_angle_1_deg7.275
r_rigid_bond_restr4.961
r_angle_refined_deg2.215
r_angle_other_deg2.101
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.971
r_dihedral_angle_4_deg18.422
r_dihedral_angle_3_deg14.982
r_dihedral_angle_1_deg7.275
r_rigid_bond_restr4.961
r_angle_refined_deg2.215
r_angle_other_deg2.101
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.015
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2473
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms21

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction