3VNB

Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago domains

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	Ammonium sulfate, citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.869	α = 90
b = 61.096	β = 90
c = 67.085	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR scanner 345 mm plate		2011-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9792	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5	50	99.9	0.069		14.1	23600	23590	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.54	100			13.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.5	45.18	23590	1262	99.91	0.18897	0.18762	0.21501	RANDOM	20.822

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]
0.12			-1.26		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.053
r_dihedral_angle_4_deg	17.603
r_dihedral_angle_3_deg	11.461
r_dihedral_angle_1_deg	5.108
r_scangle_it	3.522
r_scbond_it	2.242
r_mcangle_it	1.346
r_angle_refined_deg	1.136
r_mcbond_it	0.833
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.053
r_dihedral_angle_4_deg	17.603
r_dihedral_angle_3_deg	11.461
r_dihedral_angle_1_deg	5.108
r_scangle_it	3.522
r_scbond_it	2.242
r_mcangle_it	1.346
r_angle_refined_deg	1.136
r_mcbond_it	0.833
r_nbtor_refined	0.3
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.165
r_symmetry_vdw_refined	0.157
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1168
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	20

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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 R01GM133198.