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EphB2/SNEW Antagonistic Peptide Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 100 mM Hepes, pH 7.2, 100 mM ammonium sulfate, and 20% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.183 α = 90 b = 40.183 β = 90 c = 235.025 γ = 120
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 MARMOSAIC 300 mm CCD mirrors 2006-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 2.299 34.79 17391 17391 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) 2.299 2.3 87.06
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1NUK 2.3 34.79 17391 942 97.03 0.19793 0.19424 0.2049 0.2695 0.2774 RANDOM 33.547
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] 0.23 0.12 0.23 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_1_deg 19.432 r_dihedral_angle_3_deg 16.254 r_dihedral_angle_4_deg 16.122 r_scangle_it 2.663 r_angle_refined_deg 2.106 r_scbond_it 1.834 r_mcangle_it 1.416 r_angle_other_deg 1.295 r_mcbond_it 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_1_deg 19.432 r_dihedral_angle_3_deg 16.254 r_dihedral_angle_4_deg 16.122 r_scangle_it 2.663 r_angle_refined_deg 2.106 r_scbond_it 1.834 r_mcangle_it 1.416 r_angle_other_deg 1.295 r_mcbond_it 0.939 r_symmetry_hbond_refined 0.338 r_symmetry_vdw_other 0.263 r_chiral_restr 0.217 r_nbd_other 0.207 r_xyhbond_nbd_refined 0.2 r_nbd_refined 0.199 r_nbtor_refined 0.195 r_mcbond_other 0.178 r_symmetry_vdw_refined 0.1 r_nbtor_other 0.097 r_xyhbond_nbd_other 0.068 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2988 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing