2RF3 | pdb_00002rf3

Crystal Structure of Tricyclo-DNA: An Unusual Compensatory Change of Two Adjacent Backbone Torsion Angles

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EHV	PDB ENTRY 1EHV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	0.75 mM of oligonucleotide, 20 mM sodium cacodylate, 6 mM NaCl, 40 mM KCl and 5% MPD against 0.7 mL of 35% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.587	α = 90
b = 26.587	β = 90
c = 98.238	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC QUANTUM 315	Flat focusing mirror	2007-05-02	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A
2	SYNCHROTRON	APS BEAMLINE 5ID-B		APS	5ID-B

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	1.75	32.74	88	0.049	23.2	3.6	7823	6884

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.796	60

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EHV	1.75	32.74	6551	332	88.01	0.17829	0.17602	0.19	0.22495	0.25	RANDOM	23.477

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]
0.33	0.17		0.33		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.576
r_angle_other_deg	1.849
r_scbond_it	1.839
r_angle_refined_deg	1.757
r_nbtor_refined	0.238
r_symmetry_vdw_other	0.233
r_nbd_other	0.197
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.106
r_symmetry_hbond_refined	0.096

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	492
Solvent Atoms	93
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
CNS	refinement

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.