1YZD | pdb_00001yzd

Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43	α = 90
b = 43	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++		2004-02-24	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	2.18	31.7	91.4	0.077	0.06	15.2	21.79	7277	6646		1	28.7

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)
	2.18	2.28	57.4		0.387	0.37	3.37		405

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	2.35	8.07	5567	5556	301	98	0.265	0.236	0.236	0.22	0.292	0.28	RANDOM	30.5

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]
4.45	2.19		4.45		-8.91

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	6.9
c_scangle_it	1.92
c_scbond_it	1.46
c_improper_angle_d	1.33
c_angle_deg	0.9
c_bond_d	0.005
c_mcbond_it
c_mcangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1011
Solvent Atoms	29
Heterogen Atoms	1

Software

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