6LN3

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.6	293	0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.6, 25% (w/v) Polyethylene glycol monomethyl ether 2000, 5 mM adenosine 5'-triphosphate, 5 mM magnesium ions

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.44	α = 90
b = 193.44	β = 90
c = 193.44	γ = 90

Symmetry
Space Group	F 4 3 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		2007-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.0	SPring-8	BL26B2

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	50	96.9	0.068	79.6	37.8		20843

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	2.07	80.5		0.306	11.4	25.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1KHT	2	32.7	19709	1062	96.7	0.1612	0.1596	0.1918	RANDOM	24.776

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.93
r_dihedral_angle_4_deg	15.122
r_dihedral_angle_3_deg	14.22
r_dihedral_angle_1_deg	5.917
r_mcangle_it	2.958
r_angle_other_deg	2.286
r_mcbond_it	2.201
r_mcbond_other	2.199
r_angle_refined_deg	1.959
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.93
r_dihedral_angle_4_deg	15.122
r_dihedral_angle_3_deg	14.22
r_dihedral_angle_1_deg	5.917
r_mcangle_it	2.958
r_angle_other_deg	2.286
r_mcbond_it	2.201
r_mcbond_other	2.199
r_angle_refined_deg	1.959
r_chiral_restr	0.099
r_bond_other_d	0.034
r_bond_refined_d	0.015
r_gen_planes_other	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1543
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	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 R01GM133198.