☰ Navigation Tabs
cryo-EM structure of the NavCt voltage-gated sodium channel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 pH 9.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115 α = 90 b = 115 β = 90 c = 118 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 electron 77 2010-11-05
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 9 115 76.7 1369 250
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-Free (Depositor) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY THROUGHOUT 3RVY 9 115 1369 67 76.7 0.497 0.497 0.473 RANDOM 30
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 c_dihedral_angle_d 15.6 c_angle_deg 1 c_improper_angle_d 0.77 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 15.6 c_angle_deg 1 c_improper_angle_d 0.77 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3464 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MRC model building CNS refinement MRC data scaling MRC phasing
Sample NavCt voltage-gated sodium channel
Specimen Preparation Sample Aggregation State 2D ARRAY Vitrification Instrument LEICA KF80 Cryogen Name NITROGEN Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 9 Resolution Method OTHER Other Details Refinement Type Symmetry Type 2D CRYSTAL
Data Acquisition Detector Type KODAK SO-163 FILM Electron Dose (electrons/Å**2) 20
Imaging Experiment 1 Date of Experiment 2010-11-05 Temperature (Kelvin) Microscope Model JEOL KYOTO-3000SFF Minimum Defocus (nm) 910 Maximum Defocus (nm) 3820 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 40000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details