2P6N

Human DEAD-box RNA helicase DDX41, helicase domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.529325% PEG 3350, 200mM Lithium sulfate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.50
Crystal Properties
Matthews coefficientSolvent content
2.4148.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.013α = 90
b = 68.013β = 90
c = 305.604γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315DOUBLE CRYSTAL, SI(111) OR SI(311), TOROIDAL MIRROR2006-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.63099.90.1030.02935.94013827
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)
12.62.81000.450.08412.641.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2I4I2.629.72132206961000.245940.243450.29431RANDOM47.341
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.956
r_dihedral_angle_4_deg24.418
r_dihedral_angle_3_deg18.747
r_dihedral_angle_1_deg6.343
r_scangle_it2.548
r_scbond_it1.612
r_angle_refined_deg1.602
r_mcangle_it0.942
r_angle_other_deg0.909
r_mcbond_it0.635
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.956
r_dihedral_angle_4_deg24.418
r_dihedral_angle_3_deg18.747
r_dihedral_angle_1_deg6.343
r_scangle_it2.548
r_scbond_it1.612
r_angle_refined_deg1.602
r_mcangle_it0.942
r_angle_other_deg0.909
r_mcbond_it0.635
r_nbd_refined0.25
r_symmetry_vdw_other0.246
r_symmetry_hbond_refined0.218
r_symmetry_vdw_refined0.216
r_nbd_other0.196
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.15
r_mcbond_other0.123
r_nbtor_other0.093
r_chiral_restr0.084
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.003
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 Atoms2481
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing