2FIL | pdb_00002fil

Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-faT-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and 2'-Fluoroarabino-Thymidine (faT)

X-RAY DIFFRACTION

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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, 6 mM NaCl and 80 mM KCl., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.733	α = 90
b = 69.18	β = 92.21
c = 32.831	γ = 90

Symmetry
Space Group	P 1 21 1

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	1.0	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	1.69	30	95.4	0.094	8.1		15695	15695

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	1.69	1.8	95.8		0.347	2.8

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 (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	1.69	30	15695	15695	805	95.7	0.20401	0.20341	0.21	0.21543	0.2	RANDOM	35.247

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]
1.83		0.35	-3.9		2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	9.395
r_scbond_it	8.055
r_angle_refined_deg	2.59
r_angle_other_deg	1.881
r_xyhbond_nbd_refined	0.454
r_nbd_other	0.337
r_symmetry_hbond_refined	0.316
r_symmetry_vdw_other	0.292
r_nbd_refined	0.285
r_nbtor_refined	0.285
r_chiral_restr	0.226
r_symmetry_vdw_refined	0.192
r_nbtor_other	0.123
r_xyhbond_nbd_other	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_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	819
Solvent Atoms	169
Heterogen Atoms	49

Software

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