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Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 277 0.1 M Sodium Cacodylate pH 5.8, 150 mM Calcium Chloride
Crystal Properties Matthews coefficient Solvent content 4.11 70.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.655 α = 90 b = 105.655 β = 90 c = 193.767 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 ADSC QUANTUM 315r 2013-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 2.701 46.38 99 0.1845 0.199 0.996 9.18 7 33423
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.701 2.798 99 3.498 0.171 0.6 7
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5T4M 2.701 46.38 1.33 33258 2113 95.22 0.2015 0.2048 0.2387 0.2413
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 13.036 f_angle_d 0.754 f_chiral_restr 0.028 f_bond_d 0.012 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5354 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling Coot model building PHENIX phasing