Crystal structure of the substrate binding domain of E.coli DnaK in complex with the antimicrobial peptide oncocin
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4 | 292 | 2.4 M ammonium sulfate, 0.1 M citric acid, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.67 | 53.96 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 77.664 | α = 90 |
| b = 161.137 | β = 90 |
| c = 44.629 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
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 | MAR CCD 165 mm | 2010-06-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.3 | BESSY | 14.3 | |
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 | 2.25 | 25 | 97.7 | 0.071 | 17.7 | 4.6 | 25775 | -3 | 35.5 | ||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.28 | 25 | 24726 | 1010 | 97.6 | 0.213 | 0.211 | 0.22 | 0.284 | 0.29 | RANDOM | 35.289 | |||||
| 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] | |
| -2.91 | -0.11 | 3.02 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.687 |
| r_dihedral_angle_4_deg | 18.945 |
| r_dihedral_angle_3_deg | 18.59 |
| r_dihedral_angle_1_deg | 6.445 |
| r_scangle_it | 4.288 |
| r_scbond_it | 2.678 |
| r_angle_refined_deg | 1.855 |
| r_mcangle_it | 1.362 |
| r_mcbond_it | 0.771 |
| r_chiral_restr | 0.122 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3307 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 148 |
| Heterogen Atoms | 30 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MAR345 | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
