1P1Y | pdb_00001p1y

Crystal structure of a continuous three-dimensional DNA lattice from d(GGACAGATGGGAG)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295.5	magnesium formate, mpd, lithium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.63	α = 90
b = 40.63	β = 90
c = 55.27	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.92002	NSLS	X8C

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	1.8	50	99	0.071	0.071	20.7		5957	3066

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	2.1	2.18	99.4		0.22	13.76		307

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	35.14	2	2907	2870	161	98.7	0.20485	0.20485	0.20332	0.2	0.23256	0.24	RANDOM	39.727

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]
-1.5	-0.75		-1.5		2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	3.133
r_nbd_refined	0.381
r_xyhbond_nbd_refined	0.187
r_chiral_restr	0.12
r_symmetry_vdw_refined	0.113
r_symmetry_hbond_refined	0.065
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	257
Solvent Atoms	23
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing