5KB6

High-resolution structure of the adenosine kinase from Mus musculus in complex with adenosine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291	50% (v/v) PEG400 0.2 M lithium sulphate 0.1 M sodium acetate 2.5 mM adenosine

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.839	α = 90
b = 82.159	β = 92.69
c = 89.189	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	MARMOSAIC 225 mm CCD		2013-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	0.954	LNLS	W01B-MX2

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	1.2	50	99.8	0.054	12	4		228026

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	1.2	1.22	99.9		0.653		3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.2	20.76	216557	11429	99.72	0.1417	0.1408	0.1589	RANDOM	19.828

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]
0.22		-0.13	-0.1		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.583
r_sphericity_free	29.46
r_dihedral_angle_4_deg	14.657
r_dihedral_angle_3_deg	11.577
r_sphericity_bonded	11.226
r_dihedral_angle_1_deg	5.671
r_rigid_bond_restr	1.963
r_mcangle_it	1.514
r_angle_refined_deg	1.387
r_mcbond_it	1.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.583
r_sphericity_free	29.46
r_dihedral_angle_4_deg	14.657
r_dihedral_angle_3_deg	11.577
r_sphericity_bonded	11.226
r_dihedral_angle_1_deg	5.671
r_rigid_bond_restr	1.963
r_mcangle_it	1.514
r_angle_refined_deg	1.387
r_mcbond_it	1.099
r_mcbond_other	1.095
r_angle_other_deg	0.918
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5390
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	176

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing
DENZO	data reduction

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.