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Crystal structure of the EphB2 extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FL7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.1 M Na Succinate, 0.1M Na Acetate pH 4.8, 5% (v/v) MPD, and 3% 1, 6-Hexanediol
Crystal Properties Matthews coefficient Solvent content 5.53 77.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.843 α = 90 b = 111.142 β = 90 c = 156.877 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2013-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.145 48.4 98 0.041 0.057 0.03 18 3.3 22540 22540 116.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.145 3.32 99.3 0.792 0.792 1.04 0.544 1 3.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3FL7 3.15 48.4 1.34 22492 1151 97.23 0.2153 0.2136 0.2138 0.248 0.2439 115.9915
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4072 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing