3LCC
Structure of a SAM-dependent halide methyltransferase from Arabidopsis thaliana
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | 2.0M (NH4)2SO4, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.14 | 42.39 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 54.43 | α = 90 |
| b = 54.43 | β = 90 |
| c = 263.5 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 2 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 210 | 2009-06-12 | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9334 | ESRF | ID14-1 |
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 | 1.8 | 47.137 | 100 | 0.108 | 7.6 | 22767 | 22767 | ||||||||||||
| 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 | 1.8 | 1.9 | 100 | 0.193 | 7.9 | 5.9 | 3197 | ||||||||||||
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 | 2GB4 | 1.8 | 19.98 | 22625 | 1159 | 99.99 | 0.151 | 0.149 | 0.177 | RANDOM | 8.351 | ||||||
| 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] | |
| 0.03 | 0.02 | 0.03 | -0.05 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.226 |
| r_dihedral_angle_4_deg | 14.867 |
| r_dihedral_angle_3_deg | 11.047 |
| r_dihedral_angle_1_deg | 5.869 |
| r_scangle_it | 2.951 |
| r_scbond_it | 1.75 |
| r_angle_refined_deg | 1.285 |
| r_mcangle_it | 1.058 |
| r_angle_other_deg | 0.836 |
| r_mcbond_it | 0.558 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1697 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 198 |
| Heterogen Atoms | 27 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
| DM | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
