7APU

Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	291.15	AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl. Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant buffer containing 30% PEG 4000, 0.2 M NH4CH3CO2 (Ammonium Acetate), buffered with 100 mM CH3COONa (Sodium Acetate) adjusted to pH 4.6.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.754	α = 90
b = 82.226	β = 90
c = 78.783	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 6M		2015-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97498	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.36	44.81	98.1	0.062	0.067	0.025	0.999	14.7	7.3		99761			16.56

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.36	1.41	96		1.017	1.094	0.397	0.682	1.9	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1AKE	1.36	44.81	1.33	99721	5028	97.82	0.1854	0.1843	0.206	21.65

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
f_dihedral_angle_d	18.8035
f_angle_d	1.5641
f_chiral_restr	0.1007
f_bond_d	0.0137
f_plane_restr	0.0119

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3312
Nucleic Acid Atoms
Solvent Atoms	589
Heterogen Atoms	110

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.