4NFQ | pdb_00004nfq

Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing 7-triazolyl-8-aza-7-deazaadenosine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294.15	10% MPD(v/v) (Drop), 20% MPD(v/v) (reservoir), 40mM Na-cacodylate trihydrate (pH 7), 12mM spermine tetrahydrochloride, 80mM KCl, 10mM MgCl2 hexahydrate , VAPOR DIFFUSION, SITTING DROP, temperature 294.15K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.36	α = 90
b = 44.38	β = 121.97
c = 48.83	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	100	CCD	ADSC QUANTUM 315		2013-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.127	SSRL	BL7-1

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	1.7	36.79	93.7	0.025	16.42	1.88	15661	14671

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	1.7	1.74	88.6		0.314	2.27	1.69	1133

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	1.7	36.79	14671	13931	740	94.08	0.22383	0.22383	0.2227	0.23	0.24351	0.25	RANDOM	38.673

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]
2.6		-1.73	3.04		-2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_other_deg	3.42
r_angle_refined_deg	2.503
r_chiral_restr	0.114
r_gen_planes_refined	0.017
r_bond_refined_d	0.012
r_bond_other_d	0.009
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1026
Solvent Atoms	78
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement

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.