3CBF | pdb_00003cbf

Crystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus HB27

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z1Y	PDB ENTRY 2Z1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	18% PEG3350, 0.2M potassium fluoride, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.279	α = 90
b = 93.243	β = 90
c = 150.88	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	CCD	ADSC QUANTUM 4	mirrors	2008-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	0.978	Photon Factory	BL-6A

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	1.67	50	100	0.066	0.066	30.1	6.6	91233	91233	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.67	1.73	100		0.556	0.556		6.6	8322

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 2Z1Y	1.67	34.69	83725	83725	4415	96.77	0.20415	0.20415	0.20191	0.2	0.24709	0.25	RANDOM	23.772

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]
			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.507
r_dihedral_angle_4_deg	19.835
r_dihedral_angle_3_deg	16.109
r_dihedral_angle_1_deg	5.641
r_scangle_it	3.529
r_scbond_it	2.212
r_angle_refined_deg	1.491
r_mcangle_it	1.359
r_mcbond_it	0.854
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.507
r_dihedral_angle_4_deg	19.835
r_dihedral_angle_3_deg	16.109
r_dihedral_angle_1_deg	5.641
r_scangle_it	3.529
r_scbond_it	2.212
r_angle_refined_deg	1.491
r_mcangle_it	1.359
r_mcbond_it	0.854
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.172
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6156
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	52

Software

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