3DW0
Crystal structure of the class A carbapenemase KPC-2 at 1.6 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1DY6 | PDB entry 1DY6 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 291 | 20% PEG 6000, 0.1 M KSCN, 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.77 | 55.65 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 56.3 | ¦Á = 90 |
| b = 91.3 | ¦Â = 112.6 |
| c = 73.1 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 77 | IMAGE PLATE | MAR scanner 345 mm plate | mirror 1, double crystal, mirror 2 | 2006-07-24 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.97900 | ESRF | BM30A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.6 | 19.76 | 96.5 | 0.05 | 21.54 | 3.3 | 86680 | 14.2 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1.6 | 1.7 | 95.2 | 0.137 | 11.68 | 3 | 14100 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1DY6 | 1.6 | 19.76 | 82347 | 4335 | 100 | 0.18875 | 0.18758 | 0.2108 | RANDOM | 10.889 | ||||||
| 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] | |
| -0.02 | -0.22 | 0.36 | -0.51 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.886 |
| r_dihedral_angle_4_deg | 15.125 |
| r_dihedral_angle_3_deg | 11.953 |
| r_dihedral_angle_1_deg | 5.478 |
| r_sphericity_free | 4.654 |
| r_scangle_it | 3.059 |
| r_sphericity_bonded | 2.353 |
| r_scbond_it | 2.125 |
| r_mcangle_it | 1.375 |
| r_angle_refined_deg | 1.255 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3953 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 306 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Xnemo | data collection |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
