9GIH | pdb_00009gih

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14047

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		293	0.09M Halogens, 0.1M MOPS/HEPES-Na pH 7.5, 50% v/v EDO_P8K (Morpheus Screen, Molecular Dimensions).

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.976	α = 90
b = 80.764	β = 90
c = 166.815	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		2024-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	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	2.27	83.407	98.1	0.989	14.1	13.3		49693

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	2.27	2.31			0.759

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	2.271	83.407	49653	2417	97.993	0.211	0.2081	0.2082	0.2666	0.2667	62.272

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]
-0.321			1.191		-0.871

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.291
r_dihedral_angle_6_deg	15.072
r_lrange_it	12.82
r_lrange_other	12.803
r_dihedral_angle_2_deg	11.068
r_scangle_it	10.33
r_scangle_other	10.288
r_mcangle_other	8.891
r_mcangle_it	8.89
r_scbond_it	7.294
r_dihedral_angle_1_deg	7.235
r_scbond_other	7.189
r_mcbond_it	6.31
r_mcbond_other	6.307
r_angle_refined_deg	1.638
r_angle_other_deg	0.567
r_symmetry_nbd_refined	0.335
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_other	0.23
r_nbd_refined	0.227
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.141
r_ncsr_local_group_2	0.136
r_ncsr_local_group_1	0.124
r_ncsr_local_group_3	0.124
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.053
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	7476
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	24

Software

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