7Z3Y

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013545

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.12M Alcohols, 0.1M Buffer System 2 pH 7.5, 30.0% v/v EDO_P8K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.995	α = 90
b = 81.831	β = 90
c = 168.952	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	73	100	0.999	12.8	13.3		47609

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			0.562

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6G3Y	2.35	57.632	47513	2300	99.91	0.262	0.2597	0.31	74.348

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]
-2.078			1.807		0.271

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.547
r_dihedral_angle_4_deg	17.55
r_dihedral_angle_3_deg	14.947
r_lrange_it	5.98
r_lrange_other	5.971
r_dihedral_angle_1_deg	5.354
r_mcangle_it	3.352
r_mcangle_other	3.352
r_scangle_it	2.593
r_scangle_other	2.593
r_mcbond_it	1.923
r_mcbond_other	1.923
r_scbond_it	1.462
r_scbond_other	1.462
r_angle_refined_deg	1.165
r_angle_other_deg	1.06
r_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.166
r_symmetry_nbd_other	0.155
r_nbd_refined	0.153
r_nbtor_refined	0.149
r_xyhbond_nbd_refined	0.125
r_symmetry_nbd_refined	0.088
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.034
r_symmetry_xyhbond_nbd_other	0.012
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	7121
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	41

Software

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