2BBA

Crystal Structure and Thermodynamic Characterization of the EphB4 Receptor in Complex with an ephrin-B2 Antagonist Peptide Reveals the Determinants for Receptor Specificity.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NUKPDB entry 1NUK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.82932.2 M Ammonium Sulfate, 200 mM NaCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0960.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.972α = 90
b = 60.972β = 90
c = 151.681γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.65400.03942.73.73278611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.710.2087.23.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1NUK1.6540231786353399.920.190.17610.174360.19135RANDOM11.498
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]
0.210.21-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.303
r_dihedral_angle_4_deg16.174
r_dihedral_angle_3_deg10.131
r_dihedral_angle_1_deg7.475
r_scangle_it3.968
r_scbond_it2.79
r_angle_refined_deg1.731
r_mcangle_it1.73
r_mcbond_it1.276
r_angle_other_deg0.888
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.303
r_dihedral_angle_4_deg16.174
r_dihedral_angle_3_deg10.131
r_dihedral_angle_1_deg7.475
r_scangle_it3.968
r_scbond_it2.79
r_angle_refined_deg1.731
r_mcangle_it1.73
r_mcbond_it1.276
r_angle_other_deg0.888
r_symmetry_hbond_refined0.513
r_mcbond_other0.35
r_symmetry_vdw_refined0.342
r_symmetry_vdw_other0.294
r_nbd_refined0.272
r_nbd_other0.202
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.162
r_chiral_restr0.117
r_nbtor_other0.087
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1558
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing