Time-Resolved Structure of Metallo Beta-Lactamase L1 in a Complex with Non-Hydrolyzed Moxalactam (100 ms Snapshot)
X-RAY DIFFRACTION
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7L91 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 289 | Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350. | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.74 | 55.11 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 105.853 | α = 90 |
| b = 105.853 | β = 90 |
| c = 99.1 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 64 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 295 | CCD | RAYONIX MX340-HS | 2020-02-12 | L | LAUE | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 1.02-1.15 | APS | 14-ID-B |
Serial Crystallography
| Sample delivery method | ||
|---|---|---|
| Diffraction ID | Description | Sample Delivery Method |
| 1 | Nylon Mesh | fixed target |
| Fixed Target | ||||||
|---|---|---|---|---|---|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
| 1 | ALEX mesh holder | nylon mesh | xyz stage | SmarAct Motors viaPMAC start/stop raster over area | ||
| Data Reduction | ||||
|---|---|---|---|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
| 1 | 191 | 2746 | 191 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.2 | 31.08 | 74.7 | 0.134 | 19.9 | 11.8 | 12754 | 10.17 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.2 | 2.3 | 0.112 | ||||||||||||||||
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-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7L91 | 2.2 | 31.08 | 12691 | 583 | 73.96 | 0.2036 | 0.2016 | 0.2025 | 0.2453 | 0.2502 | 15.25 | |||||
| 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 | 19.2549 |
| f_angle_d | 0.5261 |
| f_chiral_restr | 0.0398 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1986 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 84 |
| Heterogen Atoms | 25 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| Precognition | data reduction |
| Epinorm | data scaling |
| MOLREP | phasing |














