3E58
Crystal structure of putative beta-phosphoglucomutase from Streptococcus thermophilus
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 277 | 0.2M Lithium sulfate, 0.1M Tris-Cl pH 7.0, 2.0M Ammounium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.78 | 55.81 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 88.784 | α = 90 |
| b = 88.784 | β = 90 |
| c = 118.846 | 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 | CUSTOM-MADE | 2008-08-12 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97959 | APS | 19-BM |
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 | 1.86 | 50 | 100 | 0.08 | 26.74 | 10.1 | 46085 | 46069 | -3 | 18.608 | |||||||||
| 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 | 1.86 | 1.88 | 100 | 0.404 | 3.76 | 7.9 | 1129 | ||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.86 | 50 | 46028 | 43701 | 2327 | 99.91 | 0.1713 | 0.1713 | 0.1698 | 0.19907 | RANDOM | 17.338 | |||||
| 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] | |
| 0.32 | 0.16 | 0.32 | -0.48 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.556 |
| r_dihedral_angle_3_deg | 12.166 |
| r_dihedral_angle_4_deg | 9.92 |
| r_dihedral_angle_1_deg | 5.347 |
| r_scangle_it | 3.239 |
| r_scbond_it | 2.04 |
| r_angle_refined_deg | 1.191 |
| r_mcangle_it | 1.065 |
| r_mcbond_it | 0.7 |
| r_nbtor_refined | 0.306 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3317 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 364 |
| Heterogen Atoms | 33 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
