9F8U | pdb_00009f8u

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH7399

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.09 M NPS, 0.1 M imidazole/MES pH 6.5, 50 % MPD_P1K_P3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.371	α = 90
b = 81.769	β = 90
c = 169.985	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 EIGER2 XE 16M		2023-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	2.5	58.7	100	1	19.8	13.8		40082

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	2.5	2.6			0.597

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	2.5	58.7	40018	2092	99.99	0.24	0.2367	0.2363	0.2967	0.2972	90.722

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]
0.795			0.891		-1.686

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.736
r_dihedral_angle_6_deg	13.938
r_lrange_it	11.275
r_lrange_other	11.275
r_mcangle_it	8.339
r_mcangle_other	8.338
r_scangle_it	7.161
r_scangle_other	7.145
r_dihedral_angle_other_2_deg	6.721
r_dihedral_angle_1_deg	6.636
r_mcbond_it	5.262
r_mcbond_other	5.261
r_scbond_it	4.437
r_dihedral_angle_2_deg	4.426
r_scbond_other	4.417
r_angle_refined_deg	0.92
r_angle_other_deg	0.326
r_symmetry_xyhbond_nbd_refined	0.267
r_nbd_other	0.214
r_nbd_refined	0.202
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.158
r_xyhbond_nbd_refined	0.152
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.047
r_gen_planes_refined	0.004
r_bond_refined_d	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	7494
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	18

Software

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