6G3Y

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH5675

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.09 M Halogens, 0.1 M Buffer System 2 pH 7.5, 50 % v/v Precipitant Mix 3 (Morpheus screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.817	α = 90
b = 81.357	β = 90
c = 169.157	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 PILATUS3 6M		2018-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.51	84.58	99.6	0.116	0.126	0.047	0.976	9.3	7		38585

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)	Redundancy	Number Unique Reflections (All)
1	2.51	2.56	89.6		0.852	0.918	0.338	0.137	1.8	7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1EBM	2.51	84.58	36660	1862	99.49	0.23635	0.23416	0.28215	RANDOM	73.336

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]
0.67			0.25		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.074
r_dihedral_angle_4_deg	16.145
r_dihedral_angle_3_deg	13.496
r_long_range_B_refined	6.859
r_long_range_B_other	6.859
r_dihedral_angle_1_deg	5.713
r_mcangle_it	4.58
r_mcangle_other	4.58
r_scangle_other	3.578
r_mcbond_it	2.634
r_mcbond_other	2.633
r_scbond_it	2.032
r_scbond_other	2.031
r_angle_refined_deg	1.158
r_angle_other_deg	0.893
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	7531
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	86

Software

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