5F64
Putative positive transcription regulator (sensor EvgS) from Shigella flexneri
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3F6C | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 289 | 0.2 M tri-sodium citrate, 0.1 M TRIS buffer, 15% PEG-400 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.51 | 72.71 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 168.485 | α = 90 |
| b = 110.867 | β = 126.74 |
| c = 110.769 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 | ADSC QUANTUM 315r | 2009-06-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9792 | APS | 19-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.7 | 40 | 99.3 | 0.081 | 0.095 | 0.049 | 9.8 | 3.8 | 43850 | 43850 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.7 | 2.75 | 95 | 0.83 | 0.978 | 0.512 | 0.793 | 1.7 | 3.5 | 2060 | |||||||||
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) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3F6C | 2.71 | 39.2 | 36035 | 1928 | 85.38 | 0.1851 | 0.1831 | 0.19 | 0.2229 | 0.22 | RANDOM | 48.234 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.77 | -0.12 | -0.32 | -0.13 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.891 |
| r_dihedral_angle_4_deg | 23.501 |
| r_dihedral_angle_3_deg | 18.761 |
| r_dihedral_angle_1_deg | 5.746 |
| r_mcangle_it | 3.744 |
| r_mcbond_it | 2.275 |
| r_mcbond_other | 2.275 |
| r_angle_refined_deg | 1.548 |
| r_angle_other_deg | 0.784 |
| r_chiral_restr | 0.075 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6364 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 107 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-3000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | phasing |
