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)
Type	Source	Accession Code	Details
experimental model	PDB	6GKR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	288	Ammonium acetate 0.2M; MES 0.1M pH 6.0; PEG 3350 25%

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.75	α = 90
b = 144.75	β = 90
c = 144.5	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2016-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9677	ESRF	MASSIF-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.5	19.83	99.9	0.062	0.067	0.999	17.04	7.471		92398			26.282

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)	Redundancy	Number Unique Reflections (All)
1	1.5	1.6	99.8		0.699	0.749	0.829	2.83	7.711

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6GKR	1.5	19.83	87783	4595	99.84	0.1418	0.1399	0.1763	RANDOM	22.829

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]
0.69	0.35		0.69		-2.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.971
r_dihedral_angle_4_deg	18.422
r_dihedral_angle_3_deg	14.982
r_dihedral_angle_1_deg	7.275
r_rigid_bond_restr	4.961
r_angle_refined_deg	2.215
r_angle_other_deg	2.101
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.971
r_dihedral_angle_4_deg	18.422
r_dihedral_angle_3_deg	14.982
r_dihedral_angle_1_deg	7.275
r_rigid_bond_restr	4.961
r_angle_refined_deg	2.215
r_angle_other_deg	2.101
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2473
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	21

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.