8BQ7 | pdb_00008bq7

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH2829

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	10 % w/v PEG4000, 20 % glycerol, 0.02 M monosaccharide, 0.1 M bicine/Trizma base pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.733	α = 90
b = 82.095	β = 90
c = 169.487	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 EIGER X 16M		2021-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9762	MAX IV	BioMAX

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	2.6	72.993	100	0.998	11.4	13.4		35462

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	2.6	2.72			0.589

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	7PZ1	2.6	72.993	35384	1773	99.918	0.257	0.2549	0.26	0.3069	0.31	75.414

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]
-0.401			2.914		-2.514

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.653
r_dihedral_angle_6_deg	11.195
r_lrange_it	5.672
r_lrange_other	5.665
r_dihedral_angle_1_deg	5.375
r_mcangle_it	3.474
r_mcangle_other	3.473
r_scangle_it	2.666
r_scangle_other	2.666
r_dihedral_angle_2_deg	2.543
r_mcbond_it	1.983
r_mcbond_other	1.981
r_scbond_it	1.512
r_scbond_other	1.512
r_angle_refined_deg	0.653
r_angle_other_deg	0.233
r_nbtor_refined	0.171
r_nbd_refined	0.17
r_symmetry_nbd_other	0.168
r_nbd_other	0.136
r_xyhbond_nbd_refined	0.117
r_symmetry_nbd_refined	0.103
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_refined	0.054
r_chiral_restr	0.032
r_chiral_restr_other	0.01
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6953
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	24

Software

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