1YTU | pdb_00001ytu

Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W9H	pdb entry 1w9H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 4K, potassium chloride, magnisium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.88	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 238.747	α = 90
b = 238.747	β = 90
c = 52.042	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH		2005-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	0.9776	NSLS	X26C

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	2.5	50	99.3	0.046	0.046				38254	2	2

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	2.5	2.59	98.8		0.279

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1w9H	2.5	50	2	36055	36055	1904	99.19	0.20689	0.20392	0.2	0.26623	0.26	RANDOM	61.463

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]
-0.87	-0.44		-0.87		1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.749
r_dihedral_angle_3_deg	19.923
r_dihedral_angle_4_deg	19.249
r_dihedral_angle_1_deg	7.221
r_scangle_it	3.309
r_scbond_it	2.216
r_mcangle_it	1.834
r_angle_refined_deg	1.792
r_mcbond_it	1.208
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.749
r_dihedral_angle_3_deg	19.923
r_dihedral_angle_4_deg	19.249
r_dihedral_angle_1_deg	7.221
r_scangle_it	3.309
r_scbond_it	2.216
r_mcangle_it	1.834
r_angle_refined_deg	1.792
r_mcbond_it	1.208
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.255
r_nbd_refined	0.242
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.118
r_metal_ion_refined	0.059
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6814
Nucleic Acid Atoms	409
Solvent Atoms	57
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.