2DYW | pdb_00002dyw

A Backbone binding DNA complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	355D	355D(NDB entry: bdl084)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.19mM [d(CGCGAATTCGCG)]2, 0.19mM TriplatinNC, 31mM sodium cacodylate (pH 6.5), 9.6mM magnesium chloride, 6.9% 2-methyl-2,4-pentanediol (MPD), equilibrated against a reservoir of 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 23.675	α = 90
b = 41.692	β = 90
c = 65.651	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	175	CCD	ADSC QUANTUM 4		2003-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.05	NSLS	X26C

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	1.07	50	90.1		12.5	23727	21375	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	355D(NDB entry: bdl084)	1.13	5.5	2	20317	18995	2112	81.9	0.1879	0.1818	0.2321	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
		647.55

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.042
s_angle_d	0.022
s_anti_bump_dis_restr	0.013
s_bond_d	0.012
s_rigid_bond_adp_cmpnt	0.004
s_from_restr_planes	0.0014
s_similar_dist
s_zero_chiral_vol
s_non_zero_chiral_vol
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	125
Heterogen Atoms	50

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	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.