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Crystal Structure and Thermodynamic Characterization of the EphB4 Receptor in Complex with an ephrin-B2 Antagonist Peptide Reveals the Determinants for Receptor Specificity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUK PDB entry 1NUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 2.2 M Ammonium Sulfate, 200 mM NaCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.09 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.972 α = 90 b = 60.972 β = 90 c = 151.681 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2005-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 40 0.039 42.7 3.7 32786 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 0.208 7.2 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1NUK 1.65 40 2 31786 3533 99.92 0.19 0.1761 0.17436 0.1883 0.19135 0.189 RANDOM 11.498
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] 0.21 0.21 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.303 r_dihedral_angle_4_deg 16.174 r_dihedral_angle_3_deg 10.131 r_dihedral_angle_1_deg 7.475 r_scangle_it 3.968 r_scbond_it 2.79 r_angle_refined_deg 1.731 r_mcangle_it 1.73 r_mcbond_it 1.276 r_angle_other_deg 0.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.303 r_dihedral_angle_4_deg 16.174 r_dihedral_angle_3_deg 10.131 r_dihedral_angle_1_deg 7.475 r_scangle_it 3.968 r_scbond_it 2.79 r_angle_refined_deg 1.731 r_mcangle_it 1.73 r_mcbond_it 1.276 r_angle_other_deg 0.888 r_symmetry_hbond_refined 0.513 r_mcbond_other 0.35 r_symmetry_vdw_refined 0.342 r_symmetry_vdw_other 0.294 r_nbd_refined 0.272 r_nbd_other 0.202 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.117 r_nbtor_other 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1558 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing