5NGT | pdb_00005ngt

Crystal structure of human MTH1 in complex with inhibitor 7-(furan-2-yl)-5-methyl-1,3-benzoxazol-2-amine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZR1

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 (32% (w/v) PEG3350, 0.1 mol/L Sodium Acetate pH 4.0 and 0.2 mol/L LiSO4) in a 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.326	α = 90
b = 60.617	β = 90
c = 66.672	γ = 90

Symmetry
Space Group	P 2 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		2016-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.54	44.85	0.994	0.102	0.998	12	7.2		22455

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	1.54	1.56	96.6		1.182	0.559	1.6	7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ZR1	1.54	44.85	21343	1075	99.22	0.18588	0.18413	0.19	0.22031	0.23	RANDOM	18.577

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]
0.1			0.22		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.85
r_dihedral_angle_3_deg	12.105
r_dihedral_angle_4_deg	9.222
r_dihedral_angle_1_deg	6.406
r_long_range_B_refined	5.878
r_long_range_B_other	5.834
r_scangle_other	4.41
r_scbond_it	2.896
r_scbond_other	2.818
r_mcangle_it	2.384
r_mcangle_other	2.384
r_angle_refined_deg	1.708
r_mcbond_it	1.539
r_mcbond_other	1.532
r_angle_other_deg	0.94
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.002
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	1254
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	26

Software

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