2FYM
Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| 2 | VAPOR DIFFUSION, HANGING DROP | 8.2 | 298 | 40% MPEG 550, 0.1M HEPES, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| 3 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 8% PEG 4K, 0.2 M imidazole maleate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| 4 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 27% PEG 600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 77.054 | α = 90 |
| b = 124.201 | β = 90.58 |
| c = 96.076 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 315r | 2004-05-08 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2004-02-24 | M | SINGLE WAVELENGTH | ||||||
| 3 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2004-03-09 | M | SINGLE WAVELENGTH | ||||||
| 4 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | 2004-05-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.0 | ESRF | ID14-4 |
| 2 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.9782 | ESRF | ID29 |
| 3 | ROTATING ANODE | RIGAKU | 1.54 | ||
| 4 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.0 | 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 | ||||||||
| 1,2,3,4 | 1.6 | 20 | 91.1 | 0.034 | 13.7 | 10.3 | 216453 | 216432 | 2 | 2 | |||||||||
| 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) | |||||||||||
| 1.6 | 1.63 | 94.3 | 0.253 | 2.45 | 16.51 | ||||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Enolase structure 1E9I | 1.6 | 19.99 | 216453 | 205585 | 10847 | 90.92 | 0.16652 | 0.16472 | 0.20102 | RANDOM | 20.671 | |||||
| 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] | |
| -0.02 | -0.01 | -0.02 | 0.03 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.267 |
| r_dihedral_angle_4_deg | 18.674 |
| r_dihedral_angle_3_deg | 12.064 |
| r_dihedral_angle_1_deg | 5.413 |
| r_sphericity_free | 3.556 |
| r_scangle_it | 3.078 |
| r_sphericity_bonded | 2.843 |
| r_scbond_it | 2.697 |
| r_rigid_bond_restr | 2.495 |
| r_mcangle_it | 1.237 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 12873 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1930 |
| Heterogen Atoms | 4 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
