6GKR | pdb_00006gkr

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)
Type	Source	Accession Code	Details
experimental model	PDB	6GKP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	7.5	293	HEPES 0.1M pH 7.5; Sodium chloride 3.4M

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.509	α = 90
b = 146.61	β = 90
c = 119.57	γ = 90

Symmetry
Space Group	C 2 2 21

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		2016-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.19	84.01	98.3	0.172	0.99	7	4.4		45692

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.19	2.26	99		0.884	0.661		4.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6GKP	2.19	84.01	43383	2301	98.01	0.1617	0.1593	0.16	0.2058	0.21	RANDOM	30.27

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]
0.03			1.93		-1.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.888
r_dihedral_angle_4_deg	18.996
r_dihedral_angle_3_deg	15.162
r_dihedral_angle_1_deg	7.235
r_angle_refined_deg	1.604
r_chiral_restr	0.113
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7398
Nucleic Acid Atoms
Solvent Atoms	485
Heterogen Atoms	51

Software

Software
Software Name	Purpose
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling

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.