Experiment: 3VK8

Crystal structure of DNA-glycosylase bound to DNA containing Thymine glycol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	285	PEG 3350, Mg(NO3)2, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.737	α = 90
b = 121.617	β = 95.54
c = 80.836	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 300 mm CCD	mirrors	2008-10-25	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	Xenocs FOX 2D Multilayer mirrors	2008-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B
2	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2	35	94.2	0.133	6.7	8		96852			21.4

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	2	2.07	73.3		0.37		2.8	3775

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	2	14.96	88772	8303	87.2	0.211	0.201	0.1998	0.2076	0.2304	0.2346	from 3A46	21.482

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]
4.062		0.584	-5.424		1.362

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.067
c_mcangle_it	2.139
c_scbond_it	2.057
c_mcbond_it	1.37
c_angle_d	1.165
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4732
Nucleic Acid Atoms	1054
Solvent Atoms	444
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
CNS	phasing