3UBY

Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. Crystals were obtained upon mixing 1 uL of protein-DNA complex and 1 uL of reservoir solution (100 mM BIS-TRIS, pH 5.5, 200 mM cesium chloride and 20% polyethylene glycol (PEG) 3350) over 0.5 ml of reservoir solution. Crystals appeared after incubation for 14 days at 22 degrees C, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.168	α = 90
b = 41.168	β = 90
c = 262.546	γ = 90

Symmetry
Space Group	P 43

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 315		2006-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.116	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	66	100			26998	26998

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.053	100

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	PDB entry 1BNK	2	65.65	26998	25556	1375	92.12	0.22176	0.2194	0.26545	RANDOM	36.01

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]
0.41			0.41		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.096
r_dihedral_angle_3_deg	14.599
r_dihedral_angle_4_deg	14.494
r_scangle_it	6.684
r_scbond_it	5.26
r_dihedral_angle_1_deg	5.055
r_mcangle_it	3.499
r_mcbond_it	2.61
r_angle_refined_deg	1.104
r_chiral_restr	0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.096
r_dihedral_angle_3_deg	14.599
r_dihedral_angle_4_deg	14.494
r_scangle_it	6.684
r_scbond_it	5.26
r_dihedral_angle_1_deg	5.055
r_mcangle_it	3.499
r_mcbond_it	2.61
r_angle_refined_deg	1.104
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2967
Nucleic Acid Atoms	354
Solvent Atoms	250
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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 R01GM133198.