2FGE
Crystal structure of presequence protease PreP from Arabidopsis thaliana
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | 22% PEG 6000, 0.1M Hepes, 0.025M magnesium chloride, 0.1% beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.28 | 46.07 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 110.834 | ¦Á = 90 |
| b = 114.332 | ¦Â = 90 |
| c = 162.984 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 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 QUANTUM 4 | Khozu monochromator and toroidal Zeiss mirror | 2004-11-06 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9792 | ESRF | ID14-4 |
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 | 2.1 | 93.66 | 96.5 | 0.119 | 10.4 | 4.7 | 121080 | 116872 | 45.1 | ||||||||||
| 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) | |||||||||||
| 2.1 | 2.14 | 86.6 | 0.417 | 2.26 | 2.3 | ||||||||||||||
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 | 2.1 | 93.66 | 121080 | 116872 | 5876 | 96.51 | 0.209 | 0.209 | 0.206 | 0.256 | RANDOM | 38.443 | |||||
| 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] | |
| -0.05 | -1.34 | 1.38 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.196 |
| r_dihedral_angle_4_deg | 18.648 |
| r_dihedral_angle_3_deg | 16.627 |
| r_dihedral_angle_1_deg | 5.708 |
| r_scangle_it | 3.273 |
| r_scbond_it | 2.108 |
| r_mcangle_it | 1.325 |
| r_angle_refined_deg | 1.311 |
| r_mcbond_it | 0.904 |
| r_nbtor_refined | 0.303 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15544 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 948 |
| Heterogen Atoms | 8 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| SHELXS | phasing |
| REFMAC | refinement |
