Experiment: 3A4M

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	10mM HEPES-NaOH, 250mM KI and 21% PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.156	α = 90
b = 74.524	β = 113.37
c = 64.817	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	ADSC QUANTUM 210		2008-12-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2008-10-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A
2	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9791, 0.9794, 0.9642	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.79	50					47081			22.67

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	1.792	46.498	0.03	47054	2351	98.41	0.2114	0.2092	0.205	0.2525	0.2464	28.458

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]
-4.863		2.822	2.43		2.433

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.069
f_angle_d	1.926
f_chiral_restr	0.139
f_bond_d	0.023
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3981
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	74

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling