Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae complexed with phosphoenolpyruvate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1QR7 | CHAINS A AND B OF PDB ENTRY 1QR7 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 9 | pH 9.00 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.22 | 44.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 82 | α = 65.6 |
| b = 93.8 | β = 85.6 |
| c = 104.5 | γ = 75.4 |
| Symmetry | |
|---|---|
| Space Group | P 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 | IMAGE PLATE | MARRESEARCH | 1998-09-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 | |
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 | 1.9 | 40 | 96.3 | 0.037 | 2.01 | 210365 | -3 | ||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | CHAINS A AND B OF PDB ENTRY 1QR7 | 1.9 | 40 | 198354 | 9891 | 91.8 | 0.2079 | 0.2079 | 0.2 | 0.2612 | 0.25 | THIN SHELLS | |||||
| 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] | |
| -5.75 | 3.627 | 1.667 | -1.712 | -6.502 | 7.463 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 22.66387 |
| c_scangle_it | 4.613 |
| c_mcangle_it | 3.388 |
| c_scbond_it | 2.96 |
| c_mcbond_it | 2.05 |
| c_angle_deg | 1.30021 |
| c_improper_angle_d | 0.78448 |
| c_bond_d | 0.0061 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 20624 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1251 |
| Heterogen Atoms | 80 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| EPMR | phasing |
