3HEI

Ligand Recognition by A-Class Eph Receptors: Crystal Structures of the EphA2 Ligand-Binding Domain and the EphA2/ephrin-A1 Complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320% PEG 8,000, 100 mM Tris, pH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.483α = 84.25
b = 102.108β = 79.77
c = 135.255γ = 73.94
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-CAPS24-ID-C

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
125096.10.06918.2142.3192014
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)
122.0791.20.2732.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT250182318969696.020.17490.17180.23299RANDOM10.358
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]
-1.880.01-0.840.680.041.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.187
r_dihedral_angle_4_deg16.54
r_dihedral_angle_3_deg16.129
r_dihedral_angle_1_deg7.57
r_scangle_it5.144
r_scbond_it3.363
r_mcangle_it2.225
r_angle_refined_deg2.049
r_mcbond_it1.276
r_symmetry_vdw_refined0.356
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.187
r_dihedral_angle_4_deg16.54
r_dihedral_angle_3_deg16.129
r_dihedral_angle_1_deg7.57
r_scangle_it5.144
r_scbond_it3.363
r_mcangle_it2.225
r_angle_refined_deg2.049
r_mcbond_it1.276
r_symmetry_vdw_refined0.356
r_nbtor_refined0.314
r_nbd_refined0.263
r_symmetry_hbond_refined0.254
r_xyhbond_nbd_refined0.236
r_chiral_restr0.182
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20152
Nucleic Acid Atoms
Solvent Atoms2756
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction