6QVO

Crystal structure of human MTH1 in complex with N6-methyl-dAMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M sodium acetate pH 3.5, 26 % PEG3350, 0.2 M LiSO4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.478α = 90
b = 67.111β = 94.74
c = 117.678γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.07DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.4558.61003.26.920436
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.55

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.4558.61944497199.960.239990.237650.2855RANDOM56.268
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]
9.640.89-2.34-7.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.667
r_dihedral_angle_3_deg14.474
r_dihedral_angle_4_deg12.39
r_long_range_B_refined6.946
r_long_range_B_other6.946
r_dihedral_angle_1_deg6.048
r_mcangle_it4.292
r_mcangle_other4.292
r_scangle_other3.814
r_mcbond_it2.508
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.667
r_dihedral_angle_3_deg14.474
r_dihedral_angle_4_deg12.39
r_long_range_B_refined6.946
r_long_range_B_other6.946
r_dihedral_angle_1_deg6.048
r_mcangle_it4.292
r_mcangle_other4.292
r_scangle_other3.814
r_mcbond_it2.508
r_mcbond_other2.508
r_scbond_it2.22
r_scbond_other2.22
r_angle_refined_deg1.281
r_angle_other_deg0.84
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms4929
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing