6G40

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH9525


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52940.12 M Monosaccharides, 0.1 M Buffer System 2 pH 7.5, 50 % v/v Precipitant Mix 3 (Morpheus screen, Molecular Dimensions)
Crystal Properties
Matthew coefficientSolvent content
2.4549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.86α = 90
b = 81.335β = 90
c = 168.593γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.4981.341000.0770.0830.0320.99917.21339789
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.551000.9481.0280.3960.5252.312.8

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 REPLACEMENTTHROUGHOUT1EBM2.4981.3437771195399.940.220130.217960.26258RANDOM82.556
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]
4.12-0.34-3.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.09
r_dihedral_angle_4_deg15.842
r_dihedral_angle_3_deg13.408
r_long_range_B_other6.976
r_long_range_B_refined6.976
r_dihedral_angle_1_deg5.861
r_mcangle_other4.819
r_mcangle_it4.819
r_scangle_other3.979
r_mcbond_other2.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.09
r_dihedral_angle_4_deg15.842
r_dihedral_angle_3_deg13.408
r_long_range_B_other6.976
r_long_range_B_refined6.976
r_dihedral_angle_1_deg5.861
r_mcangle_other4.819
r_mcangle_it4.819
r_scangle_other3.979
r_mcbond_other2.84
r_mcbond_it2.839
r_scbond_it2.313
r_scbond_other2.312
r_angle_refined_deg1.138
r_angle_other_deg0.89
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_bond_other_d0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7531
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing