5NGR

Crystal structure of human MTH1 in complex with fragment inhibitor 8-(methylsulfanyl)-7H-purin-6-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 (30% (w/v) PEG6000, 0.1 mol/L Sodium Acetate pH 3.7 and 0.2 mol/L LiSO4 in a 1:1 ratio.
Crystal Properties
Matthews coefficientSolvent content
2.2946.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.902α = 90
b = 67.842β = 90
c = 82.131γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2015-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
12.248.499.90.2340.9918.16.317597
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)
12.22.271002.0070.54526.5

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 REPLACEMENTTHROUGHOUT3ZR12.248.41662592799.860.212750.210360.2539RANDOM36.83
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]
-1.35-1.042.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.767
r_dihedral_angle_4_deg15.805
r_dihedral_angle_3_deg15.507
r_long_range_B_refined8.677
r_long_range_B_other8.676
r_dihedral_angle_1_deg7.036
r_scangle_other5.961
r_mcangle_it4.695
r_mcangle_other4.694
r_scbond_it3.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.767
r_dihedral_angle_4_deg15.805
r_dihedral_angle_3_deg15.507
r_long_range_B_refined8.677
r_long_range_B_other8.676
r_dihedral_angle_1_deg7.036
r_scangle_other5.961
r_mcangle_it4.695
r_mcangle_other4.694
r_scbond_it3.809
r_scbond_other3.68
r_mcbond_it2.887
r_mcbond_other2.885
r_angle_refined_deg1.541
r_angle_other_deg0.891
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms2508
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing