5NGS

Crystal structure of human MTH1 in complex with inhibitor 6-[(2-phenylethyl)sulfanyl]-7H-purin-2-amine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	5 mmol/L compound and 6 mmol/L MgCl2 were added to MTH1. Sitting drop vapor diffusion experiments at 293K were performed, and MTH1 (9.34 mg/mL) was mixed with reservoir solution (28% (w/v) PEG8000, 0.1 mol/L Sodium Acetate pH 4.0 and 0.2 mol/L LiSO4) in a 3:5 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.18	α = 90
b = 68.373	β = 90
c = 81.121	γ = 90

Symmetry
Space Group	P 21 21 21

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-F		2016-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.85	28.2	99.9	0.068	0.999	19.8	7.2		28944

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	97		0.787	0.796	2.5	7.2

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	3ZR1	1.85	28.2	27427	1468	99.34	0.21738	0.21563	0.24832	RANDOM	28.804

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]
-1.41			-1.14		2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.419
r_dihedral_angle_3_deg	13.745
r_dihedral_angle_4_deg	12.117
r_dihedral_angle_1_deg	6.305
r_long_range_B_refined	5.445
r_long_range_B_other	5.256
r_scangle_other	3.329
r_mcangle_it	2.699
r_mcangle_other	2.698
r_scbond_it	2.082
r_scbond_other	2.082
r_mcbond_it	1.713
r_mcbond_other	1.711
r_angle_refined_deg	1.345
r_angle_other_deg	0.862
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2508
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing