3VYY | pdb_00003vyy

Structural insights into RISC assembly facilitated by dsRNA binding domains of human RNA helicase A (DHX9)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WHQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 8000, CaAc2, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.252	α = 90
b = 78.529	β = 98.81
c = 112.242	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 315r		2012-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.007	NSLS	X29A

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	2.9	50	99.5	0.086	27.7	3.2	9520	9511	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.95	94.7		0.254	5.8	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1WHQ	2.9	37.01	9511	481	99.19	0.22097	0.2189	0.2182	0.26175	0.2592	RANDOM	59.391

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]
1.83		1.99	-1.37		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.126
r_dihedral_angle_3_deg	20.953
r_dihedral_angle_4_deg	19.355
r_dihedral_angle_1_deg	6.555
r_scangle_it	1.865
r_angle_refined_deg	1.644
r_mcangle_it	1.162
r_scbond_it	1.107
r_mcbond_it	0.684
r_nbtor_refined	0.305
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.171
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1356
Nucleic Acid Atoms	1060
Solvent Atoms
Heterogen Atoms

Software

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