3TCM | pdb_00003tcm

Crystal Structure of Alanine Aminotransferase from Hordeum vulgare

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XI9	The phasing template was prepared by the CCP4 program chainsaw from the Pyrococcus furiosis Pfu-1397077-001 (PDB entry 1xi9) coordinate file and the Hv (i.e., barley) AlaAT-PfAlaAT sequence alignment.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	The protein sample was 12 mg/mL in 20 mM carbonate buffer-pH 10.5, 2.5 mM PLP, 2.5 mM cycloserine, and 2.5 mM DTT. Crystals were obtained using a 0.7 mL well composition of 22(w/v)% polyethylene glycol monomethyl ether (PGME) 5000, 0.1 M MES, 9 (v/v) % tacsimate and a 2 uL sitting drop prepared from equal volumes of protein and well solution., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.859	α = 90
b = 126.973	β = 90
c = 75.663	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARMOSAIC 300 mm CCD		2009-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.71	87.2	97.1	0.1	15	4.1	32022	31088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	98.8		0.493	2.46	4.1

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	The phasing template was prepared by the CCP4 program chainsaw from the Pyrococcus furiosis Pfu-1397077-001 (PDB entry 1xi9) coordinate file and the Hv (i.e., barley) AlaAT-PfAlaAT sequence alignment.	2.71	87.16	29484	1582	96.85	0.21779	0.21455	0.21	0.27904	0.27	RANDOM	41.172

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]
-2.13			0.59		1.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.456
r_dihedral_angle_4_deg	24.589
r_dihedral_angle_3_deg	23.108
r_dihedral_angle_1_deg	6.832
r_scangle_it	3.755
r_angle_refined_deg	2.449
r_scbond_it	2.18
r_mcangle_it	2.026
r_mcbond_it	1.233
r_chiral_restr	0.166
r_bond_refined_d	0.029
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7406
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	44

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling