X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | LIQUID DIFFUSION | 7.2 | 298 | buffer: 20 mM HEPES, 5 mM of CaCl2, and 5 mM of MnCl2; pH = 7.2. The crystal was obtained by diffusion method in glass tube sequentially put with ConA solution, pure buffer, and the ligand solution. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.99 | 69.19 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 84.173 | α = 90 |
| b = 116.028 | β = 95.98 |
| c = 84.255 | 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 | PIXEL | DECTRIS PILATUS 6M | 2013-07-09 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.918 | BESSY | 14.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.06 | 39.4 | 99.7 | 17.63 | 3.42 | 98988 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.06 | 30 | 96007 | 2981 | 99.64 | 0.2465 | 0.245 | 0.25 | 0.2953 | 0.3 | RANDOM | 21.557 | |||||
| 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] | |
| -0.48 | 0.42 | 1.37 | -0.8 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.087 |
| r_dihedral_angle_4_deg | 21.031 |
| r_dihedral_angle_3_deg | 16.418 |
| r_dihedral_angle_1_deg | 8.505 |
| r_angle_refined_deg | 2.111 |
| r_chiral_restr | 0.144 |
| r_bond_refined_d | 0.019 |
| r_gen_planes_refined | 0.011 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7236 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 114 |
| Heterogen Atoms | 244 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOLREP | phasing |
| PDB_EXTRACT | data extraction |
| REFMAC | refinement |
| XDS | data scaling |
| Coot | model building |
