8AF8
Room temperature SSX crystal structure of CTX-M-14 (5K dataset)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6GTH |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 4.5 | 293 | CTX-M-14 was produced, purified and crystallized as before, with a slight modification in crystallization conditions to obtain slightly bigger crystals which roughly match the X-ray focal spot. For this purpose, a 50% CTX-M-14 solution (22 mg/ml) was mixed with a 45% precipitant solution (40% PEG8000, 200 mM lithium sulfate, 100 mM sodium acetate, pH 4.5) and with a 5% undiluted seed stock in batch crystallization setups, resulting in crystals with a homogeneous size distribution of 11-15 um after 90 minutes. The crystals were centrifuged at 200xg for 5 min and the supernatant was replaced with a stabilization buffer (28% PEG8000, 140 mM lithium sulfate, 70 mM sodium acetate, pH 4.5) to stop further crystal growth. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.16 | α = 90 |
b = 42.16 | β = 90 |
c = 234.35 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | x-ray | 295 | PIXEL | DECTRIS PILATUS 6M | 2019-12-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.0332 | PETRA III, DESY | P11 |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | TapeDrive | injection |
Injection | |||||||
---|---|---|---|---|---|---|---|
Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
1 | TapeDrive | 1 |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 5000 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (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 | 1.55 | 17.77 | 99.98 | 0.907 | 0.23 | 3.75 | 149 | 36495 | 23.14 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.55 | 1.58 | 0.262 | 1.7 | 0.63 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6GTH | 1.55 | 14.98 | 1.33 | 36462 | 765 | 99.9 | 0.1763 | 0.1758 | 0.1988 | 34.56 |
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 | 11.9532 |
f_angle_d | 1.1761 |
f_chiral_restr | 0.0604 |
f_bond_d | 0.0113 |
f_plane_restr | 0.0079 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1940 |
Nucleic Acid Atoms | |
Solvent Atoms | 209 |
Heterogen Atoms | 15 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHENIX | phasing |