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Crystal structure of human CNTN5 FN1-FN3 domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 1M NH4H2PO4, 10% (v/v) Tacsimate pH 5.0
Crystal Properties Matthews coefficient Solvent content 4.51 72.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.77 α = 90 b = 154.518 β = 90 c = 90.417 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 300 mm CCD 2013-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.685 50 85.7 0.112 14 12 14285 63.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.685 2.8 56.3 0.418 5.9 926
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5EQ4 2.685 38.63 13807 1398 82.42 0.198 0.194 0.1953 0.2314 0.2272 95.0442
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.41 f_angle_d 1.134 f_chiral_restr 0.042 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2258 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling Coot model building PDB_EXTRACT data extraction PHASER phasing