7C4V
MicroED structure of anorthic Vancomycin at 1.05 A resolution
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1FVM |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 13.97 | α = 109.52 |
b = 18.55 | β = 97.33 |
c = 23.86 | γ = 106.58 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | 2019-06-01 |
Data Collection
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) | ||||||||||
1.05 | 1.1 | 66.9 | 0.419 | 0.949 | 3.04 | 6.83 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | THROUGHOUT | 1FVM | 1.05 | 7.875 | 2.02 | 6445 | 323 | 65.99 | 0.2335 | 0.2318 | 0.2684 | Random selection | 8.8747 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
Sample |
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Vancomycin |
Specimen Preparation | |
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Sample Aggregation State | 3D ARRAY |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | CRYSTALLOGRAPHY |
Number of Particles | |
Reported Resolution (Å) | 1.05 |
Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
Other Details | |
Refinement Type | |
Symmetry Type | 3D CRYSTAL |
Space Group Name | |
Length a | 13.97 |
Length b | 18.55 |
Length c | 18.55 |
Angle Alpha | 106.58 |
Angle Beta | 97.33 |
Angle Gamma | 106.58 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (1FVM) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 0.0286 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI F20 |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | DIFFRACTION |
Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
MODEL FITTING | CCP4 package | |
MODEL REFINEMENT | PHENIX | |
MOLECULAR REPLACEMENT | CCP4 package | |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE |