X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2JDI | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICROBATCH | 277 | 20 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM MgSO4 and 1 mM ADP, 7.7% (w/v) polyethyleneglycol 10000 dissolved in a buffer containing 100 mM 2-(N-morpholino)-ethanesulfonic acid, pH 6.0 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.48 | 64.61 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 124.218 | α = 90 |
| b = 206.35 | β = 104.85 |
| c = 130.21 | 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 PILATUS3 2M | 2017-06-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-1 |
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 | 3.2 | 90.51 | 98.2 | 0.123 | 8.1 | 3.5 | 102391 | ||||||||||||
| 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 | 3.2 | 3.25 | 97.6 | 0.565 | 3.7 | ||||||||||||||
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 | 2JDI | 3.2 | 90.51 | 94768 | 4968 | 95.59 | 0.27297 | 0.27169 | 0.27 | 0.29712 | 0.3 | RANDOM | 89.235 | ||||
| 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] | |
| 0.05 | 6.82 | -0.84 | -2.48 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.764 |
| r_dihedral_angle_3_deg | 13.725 |
| r_dihedral_angle_4_deg | 12.094 |
| r_dihedral_angle_1_deg | 5.383 |
| r_long_range_B_refined | 4.548 |
| r_long_range_B_other | 4.548 |
| r_mcangle_it | 2.76 |
| r_mcangle_other | 2.759 |
| r_scangle_other | 2.032 |
| r_mcbond_it | 1.554 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 30905 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 20 |
| Heterogen Atoms | 167 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
