7U8Y

TREX1 Structural Studies Capture Small Molecule Inhibition and Implicate Novel DNA Dynamics

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Protein was dialyzed into 20 mM MES (pH 6.5) with 50 mM NaCl. Complex was formed by incubating the protein at 5 mg/mL with 2 mM dAMP and 5 mM MnCl2. 0.3 uL protein complex at 5 mg/ml TREX1 was mixed with an equal volume of reservoir solution and placed on a bridge above 50 uL of the reservoir solution. mTREX1-dAMP crystals grew in initial conditions of 0.2 M MES monohydrate, sodium hydroxide (pH 6.2), and 20% w/v polyethylene glycol 4,000. All crystals grew within one week. After crystal formation, 4 mM TIM009 was soaked into mTREX1-dAMP crystals for 5 days. Prior to data collection crystals were dipped into reservoir solution containing 15% glycerol in preparation for cryo-cooling

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.555	α = 90
b = 127.555	β = 90
c = 80.01	γ = 120

Symmetry
Space Group	H 3

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 200K	varimax HR	2020-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	2.22	50	99.1	0.073	0.077	0.025	0.997	30.8	9.4		23262			37.4

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	2.22	2.29	89.5		0.328	0.355	0.133	0.953	5.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2OA8	2.22	45.5	22068	1194	97.29	0.18309	0.18097	0.22175	RANDOM	49.402

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]
-0.08	-0.04		-0.08		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.667
r_dihedral_angle_4_deg	16.118
r_dihedral_angle_3_deg	14.493
r_long_range_B_other	9.529
r_long_range_B_refined	9.521
r_dihedral_angle_1_deg	6.297
r_scangle_other	4.56
r_scbond_it	3.066
r_scbond_other	3.065
r_mcangle_it	2.954
r_mcangle_other	2.926
r_mcbond_it	2.077
r_mcbond_other	2.044
r_angle_refined_deg	1.343
r_angle_other_deg	1.074
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3448
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Coot	model building
CrysalisPro	data collection
HKL-3000	data reduction
HKL-3000	data scaling