9FNV | pdb_00009fnv

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH12163

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 Alcohols, 0.1 M imidazole/MES pH 6.5, 50 % EDO_P8K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.39	α = 90
b = 81.48	β = 90
c = 170.19	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		2020-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	1.0332	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	2.25	73.4	100	0.999	15.2	13.4		54738

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	2.25	2.29			0.736

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	2.25	73.4	54737	2588	99.993	0.202	0.1998	0.1996	0.2522	0.2522	57.427

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]
0.33			0.008		-0.338

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.621
r_dihedral_angle_6_deg	15.591
r_lrange_other	12.063
r_lrange_it	12.06
r_dihedral_angle_2_deg	11.177
r_scangle_it	9.216
r_scangle_other	9.215
r_mcangle_it	8.497
r_mcangle_other	8.496
r_dihedral_angle_1_deg	8.009
r_scbond_it	6.265
r_scbond_other	6.264
r_mcbond_it	5.963
r_mcbond_other	5.956
r_angle_refined_deg	1.552
r_angle_other_deg	0.524
r_nbd_refined	0.227
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.186
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.172
r_symmetry_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7522
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	55

Software

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