6RLW | pdb_00006rlw

Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EBM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.367	α = 90
b = 86.367	β = 90
c = 432.4	γ = 90

Symmetry
Space Group	P 41 21 2

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		2019-02-11	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)	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	86.4	100	0.096	0.1	0.029	1	16.5	21.8		112319

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	2.03	99.9		1.22	1.28	0.39	0.846	2.7	20.6

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	1EBM	2	84.837	111929	5560	99.859	0.225	0.2225	0.23	0.2741	0.28	41.301

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]
-0.888			-0.888		1.777

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.938
r_dihedral_angle_4_deg	16.767
r_dihedral_angle_3_deg	14.025
r_dihedral_angle_1_deg	6.74
r_lrange_it	6.344
r_lrange_other	6.34
r_scangle_it	4.121
r_scangle_other	4.121
r_mcangle_it	3.792
r_mcangle_other	3.79
r_scbond_it	2.595
r_scbond_other	2.584
r_mcbond_it	2.449
r_mcbond_other	2.449
r_angle_refined_deg	1.293
r_angle_other_deg	1.205
r_nbd_refined	0.188
r_symmetry_nbd_other	0.176
r_nbd_other	0.175
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.103
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.072
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12267
Nucleic Acid Atoms
Solvent Atoms	771
Heterogen Atoms	135

Software

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