Experiment: 5BON

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZR0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291.2	Full length NUDT15 (20 mg/ml) was crystallized in the presence of alpha-Chymotrypsin (0.2 mg/ml) in 20 mM HEPES, pH 7.5, 300 mM NaCl, 10% Glycerol, and 1 mM TCEP. Sitting drop vapour diffusion experiments at 18 degrees C were performed, and NUDT15 was mixed with reservoir solution (30% PEG3350, 0.1 M Tris pH 8.5, and 0.05 M MgCl) in a 1:1 or 1:2 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.83	α = 90.07
b = 71.676	β = 90.04
c = 82.768	γ = 73.08

Symmetry
Space Group	P 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	MARRESEARCH		2014-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9	BESSY	14.1

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	1.8	47.5	95.8	0.035	12.95	1.8		118878			28.35

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	1.9	93.9		0.747	1.4	1.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ZR0	1.799	47.598	1.96	118828	5943	95.74	0.194	0.1927	0.22	Random selection

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	21.607
f_angle_d	0.932
f_chiral_restr	0.04
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9894
Nucleic Acid Atoms
Solvent Atoms	1111
Heterogen Atoms	32

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
XDS	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.