Structure of serine-beta-lactamase CTX-M-14 following the time-resolved active site binding of boric acid, 500 ms
Serial Crystallography (SX)
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 | | 293 | 50% CTX-M-14 solution (22 mg/ml) was mixed with 45% precipitant solution (40% PEG8000, 200mM lithium sulfate, 100mM sodium acetate, pH 4.5) and with 5% undiluted seed stock in batch crystallization setups |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.11 | 41.57 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 41.84 | α = 90 |
| b = 41.84 | β = 90 |
| c = 233.28 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 32 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 295 | PIXEL | DECTRIS EIGER2 X 16M | | 2020-11-30 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.033 | PETRA III, DESY | P11 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | CFEL TapeDrive | injection |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.5 | 38.88 | 99.74 | 0.999 | 26.93 | 7186 | | 39474 | | | 20.04 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.5 | 1.52 | | | 0.191 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.53 | 38.88 | 1.34 | 37221 | 2159 | 99.81 | 0.1366 | 0.135 | 0.13 | 0.1607 | 0.16 | 30.93 |
| 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 | 13.3017 |
| f_angle_d | 1.0363 |
| f_chiral_restr | 0.0527 |
| f_bond_d | 0.0085 |
| f_plane_restr | 0.0071 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1949 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 251 |
| Heterogen Atoms | 9 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHENIX | phasing |
| Coot | model building |
