Experiment: 7TDY

The ubiquitin-associated domain of human thirty-eight negative kinase 1, flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at low protein concentration

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Previous unpublished TNK1 UBA structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	1.2 uL of 2 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 7.00, 250 mM Mg-Formate.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.221	α = 90
b = 67.221	β = 90
c = 60.888	γ = 120

Symmetry
Space Group	P 65

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		2021-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	1.53	33.61	95.11	0.04884	0.0502	0.01144	0.999	27.17	18.8		22555			29.3

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	1.53	1.585	99.96		1.029	0.999	0.2728	0.907	2.69	14.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Previous unpublished TNK1 UBA structure	1.53	33.61	1.35	22555	1082	95.13	0.2058	0.2052	0.2063	0.2174	0.2209	40.22

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	11.7895
f_angle_d	1.1634
f_chiral_restr	0.0691
f_bond_d	0.0119
f_plane_restr	0.0052

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1142
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	18

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing