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Synaptotagmin-7, C2A domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 21% t-butanol, 0.1 M Tris, 0.1 M calcium chloride, 0.125 M KCl, 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.54 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.302 α = 90 b = 55.302 β = 90 c = 89.805 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 monochromator 2014-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.698 27.651 99.7 0.054 0.022 34.6 6.6 17195 11.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.5 0.985 0.528 0.542 1.42 4.1
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 FREE R-VALUE 2D8K 1.698 27.651 1.35 16468 1638 95.72 0.148 0.1444 0.1443 0.1811 0.1798 random 17.4537
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 12.701 f_angle_d 0.675 f_chiral_restr 0.048 f_bond_d 0.017 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1138 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 55
Software Software Software Name Purpose HKL-3000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing