7AYZ | pdb_00007ayz

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with activator TH10785

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	8.5	293.15	0.06 M Divalents, 0.1 M Buffer System 3 pH 8.5, 30 % v/v Precipitant Mix 2 (Morpheus screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.833	α = 90
b = 81.802	β = 90
c = 170.643	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 PILATUS3 S 6M		2018-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9780	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.6	85.3	100	0.082	0.088	0.034	1	18.3	12.8		35633

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.72			0.986	1.07	0.412	0.87	2.2

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6G3Y	2.6	73.873	35550	1850	99.944	0.239	0.2368	0.24	0.2861	0.29	73.594

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]
-2.627			5.572		-2.945

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.737
r_dihedral_angle_4_deg	15.604
r_dihedral_angle_3_deg	13.03
r_lrange_it	7.888
r_lrange_other	7.888
r_dihedral_angle_1_deg	6.325
r_mcangle_it	5.327
r_mcangle_other	5.326
r_scangle_it	4.504
r_scangle_other	4.503
r_mcbond_it	3.202
r_mcbond_other	3.2
r_scbond_it	2.656
r_scbond_other	2.656
r_angle_refined_deg	1.227
r_angle_other_deg	1.084
r_nbd_other	0.236
r_symmetry_xyhbond_nbd_refined	0.235
r_nbd_refined	0.178
r_symmetry_nbd_other	0.172
r_symmetry_nbd_refined	0.163
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.155
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.043
r_bond_refined_d	0.003
r_gen_planes_refined	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	7381
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	61

Software

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