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Structural and biophysical characterization of the EPHB4-EPHRINB2 protein protein interaction and receptor specificity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KGY PDB ENTRY 1KGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 2.2 M Ammonium sulfate, 100 mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.085 α = 90 b = 81.085 β = 90 c = 50.945 γ = 90
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 MAR CCD 165 mm 2005-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 20 99.63 19785 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.103 99.93
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 (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 1KGY 2.05 20 1 19785 1064 99.63 0.22928 0.22567 0.2255 0.29521 0.2924 RANDOM 45.738
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] -0.19 -0.19 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.951 r_dihedral_angle_3_deg 19.495 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_1_deg 8.748 r_scangle_it 7.14 r_scbond_it 5.864 r_mcangle_it 3.431 r_mcbond_it 2.407 r_angle_refined_deg 1.78 r_angle_other_deg 1.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.951 r_dihedral_angle_3_deg 19.495 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_1_deg 8.748 r_scangle_it 7.14 r_scbond_it 5.864 r_mcangle_it 3.431 r_mcbond_it 2.407 r_angle_refined_deg 1.78 r_angle_other_deg 1.018 r_mcbond_other 0.642 r_symmetry_vdw_other 0.295 r_nbd_refined 0.21 r_nbd_other 0.208 r_xyhbond_nbd_refined 0.201 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.186 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_other 0.128 r_chiral_restr 0.105 r_nbtor_other 0.092 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2467 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing