Experiment: 3S8U

Crystal structure of a 2-azido-adenine-modified RNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DVZ	PDB ENTRY 3DVZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1 volume of [3.1M (NH4)2SO4, 50mM MOPS pH7.0, 10mM MgCl2, 10mM MnCl2] + 2 volumes of [RNA in 1mM EDTA, 10mM Tris pH8.0], VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.57	α = 90
b = 29.57	β = 90
c = 76.34	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2011-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.92	SLS	X06SA

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	1.2	30	97.5	0.114			20495	19989		-3

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	1.2	1.23	91.1		0.545	2.67		1549

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3DVZ	1.2	27.574	2.01	20495	19980	1000	97.67	0.1445	0.1428	0.1785	0.1818	RANDOM

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]
1.6349			1.6349		0.4249

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.888
f_angle_d	1.784
f_chiral_restr	0.1
f_plane_restr	0.033
f_bond_d	0.019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	581
Solvent Atoms	162
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling