2OKS | pdb_00002oks

X-ray Structure of a DNA Repair Substrate Containing an Alkyl Interstrand Crosslink at 1.65 Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EN8	PDB ENTRY 1EN8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		The purified crosslinked DNA was dissolved in a buffer containing 22 mM ammonium acetate, 11 mM tris-hydroxymethyl-aminomethane (Tris)-HCl pH 8.0, and 11 mM calcium acetate. Crystals were grown using the sitting drop vapor diffusion method at 277K, in which 3 uL of a reservoir solution containing 27% 2-3 methyl-pentadiol, 115 mM calcium acetate, and 10 mM Tris-HCl pH 8.0 was added to an equal volume of DNA solution, and the mixture was equilibrated against 700 uL of the reservoir solution. Crystals first appeared after two weeks.

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.87	α = 90
b = 24.89	β = 114.5
c = 34.35	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	IMAGE PLATE	RIGAKU RAXIS IV		2004-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	1.65	40	96.1	0.046	38.1	4.1	3043	2924			8

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	1.65	1.71	79.4		0.047	25.7	2.56	239

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1EN8	1.65	18.89	3043	2924	162	96.1	0.182	0.18	0.208	0.21	RANDOM	12.8

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]
-0.86		0.75	0.62		0.24

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.3
c_improper_angle_d	2.14
c_mcangle_it	1.89
c_mcbond_it	1.34
c_angle_deg	1.1
c_bond_d	0.012
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	203
Solvent Atoms	75
Heterogen Atoms	3

Software

Software
Software Name	Purpose
CNS	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
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.