8BVX

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13264

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	6G3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10 % w/v PEG4000, 20 % glycerol, 0.03 M ethylene glycol, 0.1 M MOPS/HEPES-Na pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.589	α = 90
b = 81.874	β = 90
c = 169.954	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2021-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9762	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.35	58.85	100	0.999	12.1	13.4		48282

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43			0.576

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	58.85	48192	2387	99.934	0.265	0.2632	0.3024	68.685

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]
-0.411			2.229		-1.819

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.232
r_dihedral_angle_6_deg	10.833
r_dihedral_angle_1_deg	5.431
r_lrange_it	4.699
r_lrange_other	4.669
r_mcangle_it	2.845
r_mcangle_other	2.844
r_scangle_it	2.193
r_scangle_other	2.193
r_dihedral_angle_2_deg	2.076
r_mcbond_it	1.586
r_mcbond_other	1.586
r_scbond_it	1.245
r_scbond_other	1.245
r_angle_refined_deg	0.659
r_angle_other_deg	0.238
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.171
r_nbd_refined	0.169
r_nbd_other	0.167
r_symmetry_xyhbond_nbd_refined	0.13
r_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.074
r_symmetry_nbd_refined	0.074
r_chiral_restr	0.033
r_chiral_restr_other	0.031
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7290
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing