4FR4

Crystal structure of human serine/threonine-protein kinase 32A (YANK1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A8X	3A8X, 3L9N and 3G51
experimental model	PDB	3L9N	3A8X, 3L9N and 3G51
experimental model	PDB	3G51	3A8X, 3L9N and 3G51

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	277	20% PEG 3350, 0.2M sodium acetate, 10% ethylene glycol, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.11	α = 90
b = 154.11	β = 90
c = 112.11	γ = 120

Symmetry
Space Group	P 32

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 2M	Kirkpatrick Baez bimorph mirror pair	2011-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91730	Diamond	I04-1

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	2.29	51.68	95.7	0.089	9.3	3.3	128341	128336			35.7

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	2.29	2.41	97.8		0.638	2	3.2	19231

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	3A8X, 3L9N and 3G51	2.29	50.44	2	128336	121915	6421	95.73	0.20636	0.20436	0.24449	RANDOM	37.803

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]
1.95	0.97		1.95		-2.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.545
r_dihedral_angle_4_deg	23.088
r_dihedral_angle_3_deg	15.797
r_dihedral_angle_1_deg	6.933
r_angle_refined_deg	1.488
r_angle_other_deg	0.776
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.545
r_dihedral_angle_4_deg	23.088
r_dihedral_angle_3_deg	15.797
r_dihedral_angle_1_deg	6.933
r_angle_refined_deg	1.488
r_angle_other_deg	0.776
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16848
Nucleic Acid Atoms
Solvent Atoms	1003
Heterogen Atoms	242

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.