282D | pdb_0000282d

A CONTINOUS TRANSITION FROM A-DNA TO B-DNA IN THE 1:1 COMPLEX BETWEEN NOGALAMYCIN AND THE HEXAMER DCCCGGG

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D12	PARTS FROM DIFFERENT SOURCES: E.G. DDF001, DDF019
experimental model	PDB	1D11	PARTS FROM DIFFERENT SOURCES: E.G. DDF001, DDF019

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K

Crystal Properties
Matthews coefficient	Solvent content
3.1	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.845	α = 90
b = 45.845	β = 90
c = 58.075	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	277	IMAGE PLATE	MARRESEARCH	MULTILAYER MIRROR	1994-01-01	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LURE BEAMLINE DW32		LURE	DW32

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	25	80	0.052	0.072	19	4.2		2492		2

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)
	2.3	2.5	45		0.18	3	2.5

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	PARTS FROM DIFFERENT SOURCES: E.G. DDF001, DDF019	2.4	18	2	2365		92	0.183			25.7

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
n_multtor_nbd	0.23
n_xhyhbond_nbd	0.18
n_chiral_restr	0.17
n_singtor_nbd	0.08
n_plane_restr	0.036
n_phos_bond_angle_d	0.033
n_angle_d	0.023
n_bond_d	0.011
n_phos_bond_d	0.011
n_planar_d
n_hb_or_metal_coord
n_sugar_bond_it
n_sugar_angle_it
n_phos_bond_it
n_phos_angle_it
n_bond_angle_restr
n_dihedral_angle_restr
n_impr_tor
n_sugar_bond_d
n_sugar_bond_angle_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	240
Solvent Atoms	47
Heterogen Atoms	56

Software

Software
Software Name	Purpose
AMoRE	phasing
NUCLSQ	refinement
MOSFLM	data reduction
CCP4	data reduction
SCALF	data scaling