7Z5R | pdb_00007z5r

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH012035


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G3Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.12 M Alcohols, 0.1M Buffer System 1 pH 6.5, 30.0 % v/v GOL_P4K
Crystal Properties
Matthews coefficientSolvent content
2.6353.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.459α = 90
b = 81.533β = 90
c = 170.145γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.5170.21000.9978.812.640059
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.60.586

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6G3Y2.585.0737989196099.860.239460.236670.240.293770.3RANDOM69.249
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]
0.96-1.630.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.772
r_dihedral_angle_4_deg18.784
r_dihedral_angle_3_deg15.818
r_long_range_B_refined8.407
r_long_range_B_other8.406
r_dihedral_angle_1_deg6.277
r_mcangle_it5.878
r_mcangle_other5.878
r_scangle_other5.248
r_mcbond_other3.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.772
r_dihedral_angle_4_deg18.784
r_dihedral_angle_3_deg15.818
r_long_range_B_refined8.407
r_long_range_B_other8.406
r_dihedral_angle_1_deg6.277
r_mcangle_it5.878
r_mcangle_other5.878
r_scangle_other5.248
r_mcbond_other3.653
r_mcbond_it3.652
r_scbond_it3.171
r_scbond_other3.17
r_angle_refined_deg1.242
r_angle_other_deg0.925
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms7067
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing