5OTN

Crystal structure of zebrafish MTH1 in complex with O6-methyl-dGMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HZX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION62930.2 M CaCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG6000, 2.5 mM O6-methyl-2'-dGTP, 6 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2244.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.528α = 90
b = 55.379β = 90
c = 65.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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
10.9928.3299.20.0630.99914.16.390549
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)
10.991.0194.90.930.4181.33.7

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 REPLACEMENTTHROUGHOUT5HZX0.9928.3288256221799.090.12110.120780.13331RANDOM11.181
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]
0.17-0.07-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.558
r_sphericity_free23.271
r_dihedral_angle_4_deg21.924
r_dihedral_angle_3_deg11.76
r_dihedral_angle_1_deg6.845
r_sphericity_bonded5.899
r_long_range_B_refined2.404
r_long_range_B_other2.404
r_scangle_other1.647
r_angle_refined_deg1.629
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.558
r_sphericity_free23.271
r_dihedral_angle_4_deg21.924
r_dihedral_angle_3_deg11.76
r_dihedral_angle_1_deg6.845
r_sphericity_bonded5.899
r_long_range_B_refined2.404
r_long_range_B_other2.404
r_scangle_other1.647
r_angle_refined_deg1.629
r_scbond_it1.371
r_scbond_other1.368
r_rigid_bond_restr1.263
r_mcangle_it1.113
r_mcangle_other1.113
r_angle_other_deg0.913
r_mcbond_it0.839
r_mcbond_other0.834
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1272
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing