7NTR | pdb_00007ntr

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SUBSTRATE MIMIC 3-PHENYLPROPIONATE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ABJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PREINCUBATED OVER NIGHT WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE AND 3 MILLIMOLAR DTT. DROPS MADE FROM 1 MICROLITER PROTEIN AND 1 MICROLITER RESERVOIR (225 MILLIMOLAR MGCL2, 16-20 % (W/V) PEG 3350. CRYO: RESERVOIR SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.844	α = 90
b = 103.795	β = 90
c = 110.158	γ = 90

Symmetry
Space Group	P 21 21 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		2013-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.8726	ESRF	ID29

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	2.21	75.5	99.3	0.144	0.996	9.86	5.1		39094			39

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	2.21	2.34	96.1		0.91	0.719	1.89	5.1

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	2ABJ	2.23	42.51	36147	1900	99.9	0.1735	0.1699	0.18	0.2411	0.24	RANDOM	34.72

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			0.87		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.101
r_dihedral_angle_4_deg	18.827
r_dihedral_angle_3_deg	16.758
r_dihedral_angle_1_deg	6.728
r_angle_refined_deg	1.683
r_angle_other_deg	0.866
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.101
r_dihedral_angle_4_deg	18.827
r_dihedral_angle_3_deg	16.758
r_dihedral_angle_1_deg	6.728
r_angle_refined_deg	1.683
r_angle_other_deg	0.866
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5724
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	53

Software

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

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.