2OXC

Human DEAD-box RNA helicase DDX20, DEAD domain in complex with ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.227712% PEG3350, 200 mM Sodium chloride, 100 mM Bis-Tris, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.550.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.8α = 90
b = 63.8β = 90
c = 214.3γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Toroidal mirror2006-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93300ESRFID14-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.34099.80.0570.05723.510125192125192
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)RedundancyNumber Unique Reflections (All)
1.31.599.90.4580.2335.29.643117

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QVA1.338.4611902811902862641000.153780.153780.152680.17485RANDOM9.989
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]
0.10.050.1-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.689
r_dihedral_angle_4_deg15.543
r_dihedral_angle_3_deg11.201
r_sphericity_free5.597
r_dihedral_angle_1_deg5.11
r_scangle_it3.206
r_scbond_it2.471
r_sphericity_bonded2.469
r_mcangle_it1.537
r_angle_refined_deg1.443
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.689
r_dihedral_angle_4_deg15.543
r_dihedral_angle_3_deg11.201
r_sphericity_free5.597
r_dihedral_angle_1_deg5.11
r_scangle_it3.206
r_scbond_it2.471
r_sphericity_bonded2.469
r_mcangle_it1.537
r_angle_refined_deg1.443
r_mcbond_it1.314
r_rigid_bond_restr1.114
r_angle_other_deg0.926
r_mcbond_other0.414
r_symmetry_vdw_other0.309
r_nbd_refined0.209
r_nbd_other0.186
r_symmetry_hbond_refined0.186
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.143
r_symmetry_vdw_refined0.092
r_nbtor_other0.084
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3227
Nucleic Acid Atoms
Solvent Atoms668
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing