2X10

Crystal structure of the complete EphA2 ectodomain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C8XPDB ENTRIES 3C8X, 2E7H, 1X5L
experimental modelPDB 2E7HPDB ENTRIES 3C8X, 2E7H, 1X5L
experimental modelPDB 1X5LPDB ENTRIES 3C8X, 2E7H, 1X5L

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