2EA0

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	1.8M ammonium sulfate, 0.1M sodium acetate pH 4.6-5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.58	61.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.184	α = 90
b = 76.184	β = 90
c = 164.54	γ = 90

Symmetry
Space Group	P 43 2 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	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.100	NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	30		0.064	11.6	7		91763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	69.8		0.375

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	throughout	THROUGHOUT	1k3w	1.4	30	91763	91763	4863	95.8	0.16	0.1563		0.2043	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
15		2961.85

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.084
s_non_zero_chiral_vol	0.076
s_zero_chiral_vol	0.06
s_similar_adp_cmpnt	0.06
s_angle_d	0.034
s_from_restr_planes	0.0248
s_anti_bump_dis_restr	0.021
s_bond_d	0.014
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2032
Nucleic Acid Atoms	483
Solvent Atoms	412
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.