344D | pdb_0000344d

DETERMINATION BY MAD-DM OF THE STRUCTURE OF THE DNA DUPLEX D(ACGTACG(5-BRU))2 AT 1.46A AND 100K

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	243D	NDB ENTRY ADH070 (PDB ENTRY 243D)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.597	α = 90
b = 43.597	β = 90
c = 26.268	γ = 90

Symmetry
Space Group	P 43 21 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	IMAGE PLATE	MARRESEARCH	MIRROR	1996-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R		ELETTRA	5.2R

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	1.4	15	98.3	0.071	0.137	4.35		8062

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)
	1.4	1.45	60.1		0.137		1.1

Refinement

Statistics
Diffraction ID	Structure Solution 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 (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	NDB ENTRY ADH070 (PDB ENTRY 243D)	1.46		4555	4555		96.5	0.1115

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
		245

RMS Deviations
Key	Refinement Restraint Deviation
s_angle_d	0.006
s_bond_d
s_similar_dist
s_from_restr_planes
s_zero_chiral_vol
s_non_zero_chiral_vol
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_similar_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	161
Solvent Atoms	88
Heterogen Atoms

Software

Software
Software Name	Purpose
MLPHARE	phasing
DM	model building
SHELXL-96	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	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.