330D | pdb_0000330d

BASE-PAIRING SHIFT IN THE MAJOR GROOVE OF (CA)N TRACTS BY B-DNA CRYSTAL STRUCTURES

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VTD	B-DNA DODECAMER

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	277	pH 6.00, VAPOR DIFFUSION, temperature 277.00K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.89	α = 90
b = 65.89	β = 90
c = 47.09	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	258	AREA DETECTOR	SIEMENS

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

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	2.7	30	94	0.054		4.1		1710		1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	B-DNA DODECAMER	2.7	7	2	1378		69.7	0.17	0.17		34

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	29.2
x_improper_angle_d	1.83
x_angle_deg	1.27
x_bond_d	0.006
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	52
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	refinement
CORELS	refinement
ULTIMA	model building
XENGEN	data reduction
ULTIMA	phasing