3BB1
Crystal structure of Toc34 from Pisum sativum in complex with Mg2+ and GMPPNP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 296 | 0.2M di-potassiumphosphate 20% PEG3350, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.05 | 59.66 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 178.776 | α = 90 |
| b = 180.061 | β = 90 |
| c = 90.948 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
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 315 | 2006-07-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.0723 | ESRF | ID23-1 |
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 | 2.8 | 50 | 99.5 | 0.077 | 15.5 | 3.8 | 73060 | 72688 | -4 | -3 | 65.4 | ||||||||
| 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 | 2.8 | 2.85 | 95.9 | 0.471 | 2.4 | 3.4 | 3462 | ||||||||||||
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 | PDB entry 1H65 | 2.8 | 49.88 | 69019 | 3668 | 99.52 | 0.22714 | 0.2242 | 0.28231 | RANDOM | 60.756 | ||||||
| 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] | |
| 2.83 | 2.75 | -5.58 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.428 |
| r_dihedral_angle_4_deg | 20.887 |
| r_dihedral_angle_3_deg | 20.443 |
| r_dihedral_angle_1_deg | 10.524 |
| r_scangle_it | 2.77 |
| r_angle_refined_deg | 2.055 |
| r_scbond_it | 1.761 |
| r_angle_other_deg | 1.457 |
| r_mcangle_it | 1.308 |
| r_mcbond_it | 0.852 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15155 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 327 |
| Heterogen Atoms | 320 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DNA | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
