7DNS

Crystal structure of domain-swapped dimer of H5_Fold-0 Elsa; de novo designed protein with an asymmetric all-alpha topology


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52960.4 M MgCl2, 0.1 M Tris (pH 7.5), 30% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0138.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.98α = 90
b = 33.66β = 93.11
c = 58.38γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2017-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.1Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.32745.91298.70.090.0970.99713.636.41777041.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.332.4792.30.4830.5480.8712.544.48

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.32745.9121.38776738998.690.20860.20660.246957.5718
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
f_dihedral_angle_d26.636
f_angle_d0.517
f_chiral_restr0.032
f_bond_d0.003
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1422
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms6

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction