1K3W

Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		initial MODEL OF BR-URACIL-CONTAINING DNA COMPLEXED WITH ENDONUCLEASE VIII AT 2.4A RESOLUTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	288	1.8M Ammonium-sulfate, 0.1M sodium-citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
3.03	60.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.03	α = 90
b = 76.03	β = 90
c = 164.933	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		2001-02-26	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.42	40	95.2	0.083	8.9	5.5		86586

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)
	1.42	1.44	71.4		0.375		2	3191

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		FREE R	initial MODEL OF BR-URACIL-CONTAINING DNA COMPLEXED WITH ENDONUCLEASE VIII AT 2.4A RESOLUTION	1.42	10	76108	76108	8521	95.2	0.1646	0.2026	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
338		2830.41

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.092
s_non_zero_chiral_vol	0.07
s_zero_chiral_vol	0.06
s_similar_adp_cmpnt	0.039
s_angle_d	0.035
s_from_restr_planes	0.0255
s_anti_bump_dis_restr	0.022
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	2080
Nucleic Acid Atoms	381
Solvent Atoms	397
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.