2I4I

Crystal Structure of human DEAD-box RNA helicase DDX3X

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WRB	PDB ENTRY 1WRB for the DEAD domain and 2DB3 for the helicase domain
experimental model	PDB	2DB3	PDB ENTRY 1WRB for the DEAD domain and 2DB3 for the helicase domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	277	1.75M Na formate, 0.1M Tris pH 7.5, 20mM ATPgS and MgCl2, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.288	α = 90
b = 67.288	β = 90
c = 253.47	γ = 120

Symmetry
Space Group	P 31 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 315		2006-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.072	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	14.91	99.2		10.6	32841	32841

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	2.2	2.26	98.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1WRB for the DEAD domain and 2DB3 for the helicase domain	2.2	14.91	33112	32841	1751	99.18	0.18719	0.18873	0.18719	0.18	0.21822	0.21	RANDOM	52.846

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]
1.91	0.96		1.91		-2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.451
r_dihedral_angle_4_deg	18.485
r_dihedral_angle_3_deg	15.979
r_dihedral_angle_1_deg	6.456
r_scangle_it	4.166
r_scbond_it	2.656
r_mcangle_it	1.65
r_angle_refined_deg	1.584
r_mcbond_it	1.027
r_nbtor_refined	0.306
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.202
r_xyhbond_nbd_refined	0.183
r_symmetry_vdw_refined	0.154
r_chiral_restr	0.113
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3243
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing