1X82
CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS WITH BOUND 5-phospho-D-arabinonate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1PLZ | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 290 | 1.6M tri-sodium citrate, 50mM 5-phospho-D-arabinonate, 100mM MnCl2, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.8 | 31.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 84.506 | ¦Á = 90 |
| b = 42.73 | ¦Â = 120.32 |
| c = 57.308 | ¦Ã = 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 | MARRESEARCH | 2003-07-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.89843 | ESRF | BM14 |
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 | 1.5 | 21 | 94.5 | 0.054 | 30 | 3.5 | 28461 | 26896 | |||||||||||
| 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 | 1.5 | 1.53 | 90.6 | 0.314 | 1.85 | 1.8 | 1731 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 1PLZ | 1.5 | 20 | 25618 | 25618 | 1273 | 94.54 | 0.16301 | 0.16301 | 0.16078 | 0.20821 | RANDOM | 23.687 | ||||
| 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] | |
| -0.68 | -1.6 | 0.26 | -1.19 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_scangle_it | 23.212 |
| r_scbond_it | 22.009 |
| r_mcangle_it | 9.27 |
| r_dihedral_angle_1_deg | 6.909 |
| r_mcbond_it | 6.6 |
| r_angle_refined_deg | 1.232 |
| r_angle_other_deg | 0.743 |
| r_symmetry_vdw_other | 0.282 |
| r_nbd_other | 0.233 |
| r_nbd_refined | 0.197 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1528 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 246 |
| Heterogen Atoms | 15 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
