2FIJ | pdb_00002fij

Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DPL	NDB entry AD0007/PDB entry 1DPL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	Final droplet composition: 1 mM oligonucleotide, 10% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.277	α = 90
b = 32.469	β = 90
c = 66.749	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	CCD	MARRESEARCH		2003-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.60914	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	1.19	33.37	93.7	0.063	13.4		21724	21724

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	1.19	1.27	91		0.29	3.7		4020

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	NDB entry AD0007/PDB entry 1DPL	1.19	33.37	21724	21724	2208	93.69	0.15856	0.15856	0.15736	0.17	0.16922	0.17	RANDOM	12.888

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]
0.14			0.18		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.576
r_scbond_it	2.088
r_angle_refined_deg	1.26
r_angle_other_deg	1.145
r_nbd_refined	0.537
r_nbtor_refined	0.261
r_nbd_other	0.246
r_symmetry_vdw_other	0.224
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.576
r_scbond_it	2.088
r_angle_refined_deg	1.26
r_angle_other_deg	1.145
r_nbd_refined	0.537
r_nbtor_refined	0.261
r_nbd_other	0.246
r_symmetry_vdw_other	0.224
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.103
r_nbtor_other	0.088
r_chiral_restr	0.062
r_gen_planes_refined	0.015
r_bond_refined_d	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	408
Solvent Atoms	128
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
EPMR	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.