2X10

Crystal structure of the complete EphA2 ectodomain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11/3 V/V: PROTEIN, 1/3 V/V: 20 % POLYETHYLENE GLYCOL 6000, 1 M LICL, 0.1 M TRIS PH 8 1/3 V/V: 0.4 M NON-DETERGENT SULFOBETAINE 256
Crystal Properties
Matthews coefficientSolvent content
3.0459.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.92α = 93.02
b = 44.65β = 98.22
c = 93.42γ = 112.12
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
139194.90.156.51.7123406153.68
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.182.10.431.61.22

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (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 REPLACEMENTPDB ENTRIES 3C8X, 2E7H, 1X5L345.9171.981203759497.630.23880.23570.2986
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]
-35.95069.825210.3279-43.4632-5.4903-33.124
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.221
f_angle_d0.697
f_chiral_restr0.045
f_bond_d0.004
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3728
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms15

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing