3B7G

Human DEAD-box RNA helicase DDX20, Conserved domain I (DEAD) in complex with AMPPNP (Adenosine-(Beta,gamma)-imidotriphosphate)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OXC	PDB entry 2OXC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	25% PEG 3350, 200mM Ammonium acetate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.56	α = 90
b = 63.56	β = 90
c = 214.6	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	Mirrors	2007-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.00595	ESRF	ID29

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	1.9	45	99.7	0.081	0.023	32.1	20.5	40642	40642

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	100		0.126	0.041	21.3	18.2	5705

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2OXC	1.9	38.43	38606	38606	2032	100	0.17368	0.17368	0.17219	0.20219	RANDOM	14.938

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]
-0.08	-0.04		-0.08		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.981
r_dihedral_angle_4_deg	18.811
r_dihedral_angle_3_deg	12.681
r_dihedral_angle_1_deg	5.321
r_scangle_it	3.273
r_scbond_it	2.405
r_angle_refined_deg	1.648
r_mcangle_it	1.273
r_mcbond_it	1.087
r_angle_other_deg	0.995
r_symmetry_hbond_refined	0.497
r_symmetry_vdw_other	0.352
r_mcbond_other	0.262
r_nbd_refined	0.212
r_nbd_other	0.193
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_refined	0.089
r_chiral_restr	0.084
r_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3156
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	62

Software

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