4RKC | pdb_00004rkc

Psychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FSL	3FSL and 3QN6
experimental model	PDB	3QN6	3FSL and 3QN6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.2M Mg(NO3)2, 20% PEG3350, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.687	α = 90
b = 62.106	β = 102.91
c = 85.895	γ = 90

Symmetry
Space Group	P 1 21 1

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	MAR CCD 165 mm	mirrors	2011-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8020	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.19	50	99.9	0.091	0.091	16.67	5		39647		-3

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	2.19	2.27	99.3		0.386	3.72	4.3

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 (All)	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	3FSL and 3QN6	2.19	43	37644	1989	99.62	0.14517	0.14517	0.14207	0.1422	0.20316	0.202	RANDOM	25.137

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]
0.46		-0.52	0.57		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.55
r_dihedral_angle_4_deg	18.182
r_dihedral_angle_3_deg	15.348
r_long_range_B_refined	6.783
r_dihedral_angle_1_deg	6.563
r_mcangle_it	2.96
r_scbond_it	2.833
r_angle_refined_deg	2.048
r_mcbond_it	1.978
r_chiral_restr	0.135
r_bond_refined_d	0.02
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6202
Nucleic Acid Atoms
Solvent Atoms	771
Heterogen Atoms	74

Software

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