3H8O

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	PEG 8000, NaCl, MgCl2, Cacodylate buffer, pH 6.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.11	α = 90
b = 79.11	β = 90
c = 242.27	γ = 120

Symmetry
Space Group	P 65 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		2008-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0	APS	23-ID-B

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	20	99.87		20	29726	29687	2	1

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	2.05	99.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2	20	5	13	31322	29687	1600	99.89	0.2035	0.204	0.202	0.237	RANDOM	27.682

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]
0.51	0.25		0.51		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.8
r_dihedral_angle_4_deg	14.146
r_dihedral_angle_3_deg	13.569
r_dihedral_angle_1_deg	5.73
r_scangle_it	2.832
r_scbond_it	1.783
r_angle_refined_deg	1.583
r_mcangle_it	1.164
r_mcbond_it	0.652
r_chiral_restr	0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.8
r_dihedral_angle_4_deg	14.146
r_dihedral_angle_3_deg	13.569
r_dihedral_angle_1_deg	5.73
r_scangle_it	2.832
r_scbond_it	1.783
r_angle_refined_deg	1.583
r_mcangle_it	1.164
r_mcbond_it	0.652
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1650
Nucleic Acid Atoms	528
Solvent Atoms	195
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection

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.