5NGT

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2935 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 coefficientSolvent content
2.0138.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.326α = 90
b = 60.617β = 90
c = 66.672γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5444.850.9940.1020.998127.222455
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)RedundancyNumber Unique Reflections (All)
11.541.5696.61.1820.5591.67

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3ZR11.5444.8521343107599.220.185880.184130.22031RANDOM18.577
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]
0.10.22-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.85
r_dihedral_angle_3_deg12.105
r_dihedral_angle_4_deg9.222
r_dihedral_angle_1_deg6.406
r_long_range_B_refined5.878
r_long_range_B_other5.834
r_scangle_other4.41
r_scbond_it2.896
r_scbond_other2.818
r_mcangle_it2.384
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.85
r_dihedral_angle_3_deg12.105
r_dihedral_angle_4_deg9.222
r_dihedral_angle_1_deg6.406
r_long_range_B_refined5.878
r_long_range_B_other5.834
r_scangle_other4.41
r_scbond_it2.896
r_scbond_other2.818
r_mcangle_it2.384
r_mcangle_other2.384
r_angle_refined_deg1.708
r_mcbond_it1.539
r_mcbond_other1.532
r_angle_other_deg0.94
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1254
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing