1Q3B

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The R252A mutant at 2.05 resolution.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.4	288	35% PEG 400, 0.1M Tris-HCl pH 8.4, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.722	α = 90
b = 80.051	β = 90
c = 169.311	γ = 90

Symmetry
Space Group	I 2 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	MAR CCD 165 mm		2001-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.102	APS	5ID-B

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	2.05	30	99.9	0.06		5.43	25032	25032			25.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	100		0.421		5	1220

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	The Protein chain from PDB code 1K3W	2.05	29.21	25032	25024	2095	99.7	0.228	0.228	0.26	RANDOM	45.3

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]
-13.87			22.45		-8.58

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.7
c_scangle_it	3.03
c_mcangle_it	2.19
c_scbond_it	2.04
c_mcbond_it	1.37
c_angle_deg	1.2
c_improper_angle_d	0.79
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	9

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.