4BGN
cryo-EM structure of the NavCt voltage-gated sodium channel
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
Initial Refinement Model(s) | |||
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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 |
Symmetry | |
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Space Group | P 4 |
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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 |
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 |
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NavCt voltage-gated sodium channel |
Specimen Preparation | |
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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 |
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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 |