The Crystal Structure of PTS System IIA Component from Enterococcus faecalis V583
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 291 | 0.1 M Sodium acetate pH 4.6, 4% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.42 | 49.25 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 58.249 | α = 90 |
| b = 58.249 | β = 90 |
| c = 140.443 | 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 | 100 | CCD | SBC-3 | mirrors | 2005-07-25 | M | MAD | |||||
| 2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | mirrors | 2005-11-22 | M | SINGLE WAVELENGTH | |||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9793, 0.9795 | APS | 19-BM |
| 2 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9793 | APS | 19-ID |
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 | 1.57 | 34.32 | 98.7 | 0.054 | 17.3 | 12.7 | 39333 | 38988 | 23.2 | ||||||||||
| 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 | 1.57 | 1.63 | 88.4 | 0.332 | 4.5 | 8.2 | 3411 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.57 | 34.32 | 38693 | 38693 | 3615 | 98.6 | 0.174 | 0.169 | 0.169 | 0.1682 | 0.229 | 0.2254 | RANDOM | 25.4 | |||
| 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] | |
| 2.29 | 0.6 | 2.29 | -4.58 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 25.8 |
| c_scangle_it | 3.91 |
| c_scbond_it | 2.63 |
| c_mcangle_it | 2.33 |
| c_angle_deg | 1.5 |
| c_mcbond_it | 1.45 |
| c_improper_angle_d | 0.73 |
| c_bond_d | 0.007 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1844 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 257 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| SBC-Collect | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| HKL-3000 | phasing |
| MLPHARE | phasing |
| RESOLVE | phasing |
| SHELXE | model building |
| SHELXD | phasing |
