1J5X
Crystal structure of Glucosamine-6-phosphate deaminase (TM0813) from Thermotoga maritima at 1.8 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8 | 293 | 40% PEG-400, 0.1 M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 8.00 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.51 | 50.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.96 | α = 90 |
| b = 72.96 | β = 90 |
| c = 128.52 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 315 | 2001-12-11 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97980, 0.93218, 0.97999 | SSRL | BL9-2 |
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 | 1.7 | 45.054 | 99.5 | 0.07 | 26.5 | 18.3 | 39495 | 23.99 | |||||||||||
| 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 | 1.7 | 1.74 | 95.1 | 0.506 | 2.8 | 8.2 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | MAD | THROUGHOUT | 1.8 | 20 | 2 | 37372 | 37360 | 1914 | 100 | 0.192 | 0.192 | 0.231 | RANDOM | 27.7 | |||||
| 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] | |
| -4.173 | -1.479 | -4.173 | 8.345 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_scangle_it | 4.141 |
| c_scbond_it | 3.224 |
| c_mcangle_it | 2.512 |
| c_angle_deg | 1.94 |
| c_mcbond_it | 1.935 |
| c_bond_d | 0.021 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2517 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 294 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOSFLM | data reduction |
| SCALA | data scaling |
| CCP4 | data reduction |
| CCP4 | model building |
| SOLVE | phasing |
| RESOLVE | model building |
| CNS | refinement |
| CCP4 | data scaling |
| CCP4 | phasing |
| RESOLVE | phasing |
