5KB5 | pdb_00005kb5

Crystal structure of the adenosine kinase from Mus musculus in complex with adenosine and adenosine-diphosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	40% PEG400 15% PEG1000 0.15M Sodium di-potassium phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.01	34.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.264	α = 90
b = 73.559	β = 90
c = 84.33	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	MARMOSAIC 225 mm CCD		2013-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.459	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	1.8	50	97.6	0.093	9.4	4.2		28540

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	1.8	1.83	98.8		0.732		4.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1BX4	1.8	24.63	27048	1450	97.51	0.1673	0.1655	0.18	0.1999	0.21	RANDOM	24.216

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]
-0.1			-0.19		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.768
r_dihedral_angle_4_deg	16.545
r_dihedral_angle_3_deg	14.661
r_dihedral_angle_1_deg	5.705
r_angle_refined_deg	1.849
r_mcangle_it	1.098
r_angle_other_deg	1.053
r_mcbond_it	0.686
r_mcbond_other	0.686
r_chiral_restr	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.768
r_dihedral_angle_4_deg	16.545
r_dihedral_angle_3_deg	14.661
r_dihedral_angle_1_deg	5.705
r_angle_refined_deg	1.849
r_mcangle_it	1.098
r_angle_other_deg	1.053
r_mcbond_it	0.686
r_mcbond_other	0.686
r_chiral_restr	0.119
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2679
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	86

Software

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