9FNU | pdb_00009fnu

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13579

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.12 M Ethylene Glycols, 0.1 M sodium HEPES/MOPS pH 7.5, 50 % GOL_P4K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.89	α = 90
b = 81.114	β = 90
c = 170.104	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	73.2	100	0.997	13.7	13.4		76437

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	2.04			0.727

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	73.158	76300	3760	99.902	0.219	0.2168	0.2241	0.2564	0.264	57.381

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]
1.571			-1.123		-0.448

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.877
r_dihedral_angle_6_deg	15.172
r_lrange_other	10.955
r_lrange_it	10.95
r_scangle_it	8.246
r_scangle_other	8.246
r_dihedral_angle_2_deg	7.789
r_dihedral_angle_1_deg	7.289
r_mcangle_it	7.222
r_mcangle_other	7.222
r_scbond_it	5.564
r_scbond_other	5.563
r_mcbond_other	5.293
r_mcbond_it	5.292
r_angle_refined_deg	1.402
r_angle_other_deg	0.469
r_nbd_other	0.237
r_nbd_refined	0.227
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.175
r_symmetry_nbd_refined	0.148
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.051
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7394
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing