3CJZ

Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m22G:A pairs

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		canonical A-form RNA dodecamer omitting U13 and U26

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	301	2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a reservoir of 1ml of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 301K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.118	α = 90
b = 25.97	β = 97.41
c = 45.393	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 225 mm CCD		2004-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

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	1.8	44.99	93.9	0.099	26.4	2	6420	6027

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)
	1.8	1.86	81.4		0.3539	4.8	1.9	661

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	A cononical A-RNA dodecamer generated with the program TURBO-FRODO omitting U13 and U26.	1.8	44.99	6420	4816	582	84.12	0.19938	0.19005	0.27742	RANDOM	25.807

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]
-1.88		0.63	0.18		1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	1.993
r_scbond_it	1.582
r_angle_refined_deg	1.356
r_angle_other_deg	1.124
r_nbd_other	0.249
r_nbtor_refined	0.236
r_symmetry_vdw_other	0.212
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.146
r_nbd_refined	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	1.993
r_scbond_it	1.582
r_angle_refined_deg	1.356
r_angle_other_deg	1.124
r_nbd_other	0.249
r_nbtor_refined	0.236
r_symmetry_vdw_other	0.212
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.146
r_nbd_refined	0.108
r_symmetry_vdw_refined	0.084
r_nbtor_other	0.077
r_xyhbond_nbd_other	0.075
r_chiral_restr	0.051
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	556
Solvent Atoms	115
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
X-GEN	data reduction
X-GEN	data scaling
MOLREP	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.