7AZ0 | pdb_00007az0

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with TH12161

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		295	0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 30% v/v Precipitant Mix 2 (Morpheus Screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.086	α = 90
b = 81.645	β = 90
c = 169.631	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		2020-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	81.64	100	0.999	11.1	26.3		44894

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	2.49	100		0.64	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6G3Y	2.4	73.676	44815	2164	99.973	0.231	0.2296	0.24	0.2566	0.26	Random selection	65.957

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]
-1.97			-0.705		2.675

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.647
r_dihedral_angle_4_deg	16.866
r_dihedral_angle_3_deg	15.436
r_lrange_other	6.963
r_lrange_it	6.962
r_dihedral_angle_1_deg	6.697
r_mcangle_it	4.804
r_mcangle_other	4.804
r_scangle_it	4.364
r_scangle_other	4.363
r_mcbond_it	2.983
r_mcbond_other	2.983
r_scbond_it	2.63
r_scbond_other	2.63
r_angle_refined_deg	1.249
r_angle_other_deg	1.136
r_symmetry_xyhbond_nbd_refined	0.253
r_symmetry_nbd_refined	0.246
r_nbd_other	0.207
r_nbd_refined	0.183
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.145
r_ncsr_local_group_2	0.1
r_ncsr_local_group_3	0.1
r_ncsr_local_group_1	0.08
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.052
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7395
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	43

Software

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