9F8V | pdb_00009f8v

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH7420

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 Monosaccharides, 0.1 M bicine/Trizma base pH 8.5, 50 % GOL_P4K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.501	α = 90
b = 81.598	β = 90
c = 170.355	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	2.4	58.956	100	0.999	16.9	13.3		45246

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	2.4	2.48			0.774

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	2.4	58.956	45178	2258	99.982	0.232	0.2293	0.2292	0.2813	0.281	74.466

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]
1.181			-0.132		-1.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	22.398
r_dihedral_angle_3_deg	16.358
r_dihedral_angle_6_deg	16.069
r_lrange_other	15.009
r_lrange_it	15.005
r_mcangle_it	11.969
r_mcangle_other	11.969
r_scangle_it	10.827
r_scangle_other	10.826
r_mcbond_it	8.05
r_mcbond_other	8.049
r_dihedral_angle_1_deg	7.803
r_scbond_it	7.17
r_scbond_other	7.169
r_dihedral_angle_2_deg	6.517
r_angle_refined_deg	1.432
r_angle_other_deg	0.484
r_nbd_other	0.275
r_nbd_refined	0.226
r_symmetry_nbd_other	0.202
r_symmetry_nbd_refined	0.2
r_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	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	7531
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	43

Software

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