9T99 | pdb_00009t99

Structure of C. elegans Dicer-related helicase 1 (DRH1) bound to blunt end 5'P-dsRNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Directly after size exclusion chromatography DRH-1deltaN_E431Q was concentrated 10 mg/ml and mixed with 12 dsRNAp in a 1:2 molar ratio, ADP-AlF4 (adenosine-5-diphosphate with aluminium fluoride) and 2 mM MgCl2 were added then incubated for 30 minutes on ice. The complex was mixed with reservoir buffer (0.2 M tri Ammonium citrate 20 % PEG3350 or 0.2 M Sodium malonate dibasic monohydrate 20% PEG3350) in 1:1 ratio. Crystals grew in two weeks at 4 C.

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.354	α = 90
b = 134.354	β = 90
c = 221.301	γ = 90

Symmetry
Space Group	I 41 2 2

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		2016-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97931	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	114.846	84.2	0.075	0.087	0.037	0.999	11	5		44595

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.335	23		1.549	0.514	1.5	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.18	72.08	1.35	44588	2277	84.21	0.2199	0.2179	0.2177	0.2569	0.257	85.19

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.9177
f_angle_d	0.5001
f_chiral_restr	0.0387
f_plane_restr	0.0044
f_bond_d	0.0027

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5584
Nucleic Acid Atoms	748
Solvent Atoms	80
Heterogen Atoms	28

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	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.