1VL1
Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1PBT | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 0.2M (NH4)2HCitrate, 20% PEG-3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.93 | 35.71 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 37.733 | α = 90 |
| b = 75.146 | β = 90 |
| c = 148.443 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 21 |
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 | 2004-04-02 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 | |
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 | 1.55 | 50 | 79.46 | 0.075 | 16.59 | 3.86 | 24729 | 23.98 | |||||||||||
| 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 | 1.55 | 1.61 | 26.04 | 0.325 | 2.93 | 2.57 | 798 | ||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1PBT | 1.55 | 37.11 | 23466 | 1262 | 79.32 | 0.16717 | 0.16523 | 0.20395 | RANDOM | 22.367 | ||||||
| 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] | |
| -0.31 | 2.44 | -2.14 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.484 |
| r_dihedral_angle_4_deg | 16.694 |
| r_dihedral_angle_3_deg | 11.733 |
| r_dihedral_angle_1_deg | 6.249 |
| r_scangle_it | 3.979 |
| r_scbond_it | 2.733 |
| r_angle_refined_deg | 1.62 |
| r_mcangle_it | 1.535 |
| r_mcbond_it | 1.151 |
| r_angle_other_deg | 0.876 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1766 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 167 |
| Heterogen Atoms | 13 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
