Experiment: 2PKV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	115D	115D FROM PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	10 mg of lyophilized DNA dissolved in 0.2 ml of a 15 % MPD solution with additives: 10-5 M sodium azide, 10-2 M MgCl2 and 2.10-2 spermine chloride. Reservoir : same solution but 50 % MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.03	α = 90
b = 45.03	β = 90
c = 41.75	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	IMAGE PLATE	MAR scanner 345 mm plate		2006-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID27	0.3738	ESRF	ID27

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	1.6	19	94.5	0.045	9.3	4	6228	6228	2	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)
	1.6	1.7	96.2		0.33	2.3	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	115D FROM PDB	1.6	10	4	2	6228	6228	497	96.8	0.1585	0.151	0.1486	0.16	0.1891	0.15	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
	184	379

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.043
s_angle_d	0.029
s_bond_d	0.011
s_non_zero_chiral_vol	0.01
s_anti_bump_dis_restr	0.006
s_from_restr_planes	0.0012
s_similar_dist
s_zero_chiral_vol
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	322
Solvent Atoms	57
Heterogen Atoms

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
XDS	data reduction
SCALA	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 R01GM157729.