6T3V | pdb_00006t3v

Psychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with substrate analog - malic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RKC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	2.1 M DL-malic acid pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.209	α = 90
b = 90.209	β = 90
c = 241.75	γ = 120

Symmetry
Space Group	P 65 2 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 225 mm CCD		2013-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	1.62	50	97	0.056	16.1	13.6		72901

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	1.62	1.68	78.1		0.39		10

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4RKC	1.62	35	69085	3674	97.02	0.1256	0.1236	0.1637	0.1747	RANDOM	37.709

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]
0.14	0.07		0.14		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.463
r_sphericity_free	23.041
r_dihedral_angle_4_deg	19.209
r_dihedral_angle_3_deg	12.883
r_sphericity_bonded	12.527
r_dihedral_angle_1_deg	5.647
r_rigid_bond_restr	3.817
r_angle_refined_deg	1.631
r_chiral_restr	0.12
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3101
Nucleic Acid Atoms
Solvent Atoms	510
Heterogen Atoms	24

Software

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