2PL3

Human DEAD-box RNA helicase DDX10, DEAD domain in complex with ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527720% Ethanol, 50mM Sodium chloride, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3363.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.5α = 90
b = 63.5β = 90
c = 304.01γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMultilayer mirror2007-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.04123MAX III911-2

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
12.153099.70.0480.01754.125.42088920889
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)
12.152.31000.160.04724.526.53719

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2GXS2.1529.3198421984210451000.211560.209730.24757RANDOM38.392
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.855
r_dihedral_angle_3_deg15.813
r_dihedral_angle_4_deg15.476
r_dihedral_angle_1_deg6.684
r_scangle_it3.49
r_scbond_it2.248
r_angle_refined_deg1.695
r_mcangle_it1.564
r_angle_other_deg1.034
r_mcbond_it0.949
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.855
r_dihedral_angle_3_deg15.813
r_dihedral_angle_4_deg15.476
r_dihedral_angle_1_deg6.684
r_scangle_it3.49
r_scbond_it2.248
r_angle_refined_deg1.695
r_mcangle_it1.564
r_angle_other_deg1.034
r_mcbond_it0.949
r_symmetry_hbond_refined0.356
r_symmetry_vdw_other0.284
r_nbd_refined0.212
r_mcbond_other0.202
r_nbd_other0.196
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.171
r_symmetry_vdw_refined0.104
r_chiral_restr0.099
r_nbtor_other0.096
r_bond_refined_d0.017
r_gen_planes_refined0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1814
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing