1YLT
Atomic resolution structure of CTX-M-14 beta-lactamase
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1YLJ | PDB ENTRY 1YLJ |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.5 | 293 | ammonium sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.72 | 28.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 41.467 | α = 90 |
| b = 62.42 | β = 90 |
| c = 86.742 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | MIRRORS | 2004-02-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 | |
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 | 1.1 | 22 | 96.9 | 0.037 | 16.2 | 6.23 | 89046 | -3 | |||||||||||
| 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) | |||||||||||
| 1.1 | 1.14 | 76.4 | 0.276 | 2.02 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | AB INITIO | FREE R | PDB ENTRY 1YLJ | 1.1 | 22 | 81443 | 81443 | 4288 | 88.5 | 0.124 | 0.123 | 0.124 | 0.157 | RANDOM | |||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 122 | 1886 | 2391.66 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_zero_chiral_vol | 0.195 |
| s_non_zero_chiral_vol | 0.094 |
| s_approx_iso_adps | 0.05 |
| s_angle_d | 0.031 |
| s_from_restr_planes | 0.029 |
| s_similar_adp_cmpnt | 0.023 |
| s_anti_bump_dis_restr | 0.021 |
| s_bond_d | 0.014 |
| s_rigid_bond_adp_cmpnt | 0.002 |
| s_similar_dist | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2100 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 427 |
| Heterogen Atoms | 78 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELX | model building |
| SHELXL-97 | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| SHELX | phasing |
