9F8Z | pdb_00009f8z

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13677

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
2.66	53.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.643	α = 90
b = 82.369	β = 90
c = 171.967	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	85.9	94.1	1	13.9	13.8		31051

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	2.71			0.705

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	2.503	85.9	31050	1505	77.099	0.228	0.2252	0.2253	0.2771	0.2771	68.911

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]
0.462			-0.534		0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.105
r_dihedral_angle_6_deg	15.498
r_lrange_it	13.479
r_lrange_other	13.479
r_mcangle_other	10.045
r_mcangle_it	10.044
r_scangle_it	9.786
r_scangle_other	9.761
r_dihedral_angle_2_deg	9.62
r_dihedral_angle_1_deg	7.877
r_mcbond_it	6.542
r_mcbond_other	6.541
r_scbond_it	6.236
r_scbond_other	6.202
r_angle_refined_deg	1.266
r_angle_other_deg	0.43
r_nbd_refined	0.224
r_nbd_other	0.224
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.195
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.186
r_ncsr_local_group_2	0.12
r_ncsr_local_group_1	0.117
r_ncsr_local_group_3	0.114
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.06
r_symmetry_xyhbond_nbd_other	0.055
r_metal_ion_refined	0.018
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7519
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	46

Software

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