6Q00

TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	278	10 mM Tris, 200 mM Potassium Formate, 14% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.742	α = 90
b = 48.742	β = 90
c = 50.421	γ = 90

Symmetry
Space Group	P 41

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	RAYONIX MX300-HS		2015-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.8266	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	0.85	50	99.6	0.048	0.049	0.009	15.3	16.1		202939			10.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.85	0.86	97.8		0.443	0.574		8.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	0.85	28.453	1.34	202929	10141	99.38	0.0958	0.0949	0.1118	14.6

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	16.06
f_angle_d	1.469
f_chiral_restr	0.09
f_bond_d	0.015
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	954
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
HKL-2000	data collection
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.