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2.0 angstrom structure of plant Extended Synaptotagmin 1, C2A domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ANK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 12% w/v Polyethylene glycol 3350, 100 mM HEPES pH 7.5, 5 mM Cobalt (II) chloride hexahydrate, 5 mM Nickel (II) chloride hexahydrate, 5 mM Cadmium chloride hydrate and 5 mM Magnesium chloride hexahydrate.
Crystal Properties Matthews coefficient Solvent content 3.36 63.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.937 α = 90 b = 70.937 β = 90 c = 116.309 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 PIXEL DECTRIS PILATUS 6M 2020-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979178 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 42.233 99.5 0.085 0.997 7.6 3.4 14603 42.02
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 2.06 1.664 0.45
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 FREE R-VALUE 6ANK 2 42.23 1.96 14573 740 99.35 0.1872 0.186 0.1874 0.2106 0.2118 62.98
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 21.5031 f_angle_d 0.9107 f_chiral_restr 0.0533 f_bond_d 0.0076 f_plane_restr 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1074 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing