1YY0 | pdb_00001yy0

Crystal structure of an RNA duplex containing a 2'-amine substitution and a 2'-amide product produced by in-crystal acylation at a C-A mismatch

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	273	MPD, sodium cacodylate, spermidine, calcium chloride, magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.6	α = 90
b = 42.6	β = 90
c = 121	γ = 120

Symmetry
Space Group	P 31 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	100	IMAGE PLATE	RIGAKU RAXIS IV		2003-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.9	35.3	97.8	0.15	0.13	12.85		3530	3450		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.9	3	97.6		0.45	0.27	2.52		330

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.2	8.99	2225	2217	115	99.6	0.252	0.232	0.232	0.22	0.264	0.25	RANDOM	54

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]
11.32	-1.18		11.32		-22.64

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	9.7
c_improper_angle_d	1.46
c_angle_deg	1.2
c_scangle_it	1.08
c_scbond_it	0.63
c_bond_d	0.006
c_mcbond_it
c_mcangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1011
Solvent Atoms	8
Heterogen Atoms	2

Software

Software
Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
SCALEPACK	data scaling
AMoRE	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.