X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3ABD | 3ABD (Rev7 molecule only) |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 292.15 | well solution containing 100 mM sodium acetate, 200 mM NaCl, 1.4 M ammonium sulfate was mixed at 1:1 ratio with protein at 45 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.32 | 46.92 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 63.691 | α = 90 |
| b = 63.691 | β = 90 |
| c = 116.274 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 77.15 | PIXEL | DECTRIS PILATUS3 S 6M | 2016-03-04 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | CHESS BEAMLINE F1 | 0.976 | CHESS | F1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.68 | 116.27 | 99.6 | 0.063 | 0.067 | 0.022 | 40.4 | 9.3 | 31583 | ||||||||||
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 | 3ABD (Rev7 molecule only) | 1.68 | 116.27 | 31583 | 1486 | 99.6 | 0.183 | 0.181 | 0.19 | 0.223 | 0.23 | RANDOM | 47.572 | ||||
| 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] | |
| 1.8 | 0.9 | 1.8 | -5.85 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.115 |
| r_dihedral_angle_3_deg | 15.615 |
| r_dihedral_angle_4_deg | 15.456 |
| r_dihedral_angle_1_deg | 6.022 |
| r_mcangle_it | 5.423 |
| r_mcbond_it | 4.081 |
| r_mcbond_other | 4.061 |
| r_angle_other_deg | 3.515 |
| r_angle_refined_deg | 1.84 |
| r_chiral_restr | 0.115 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1857 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 140 |
| Heterogen Atoms | 18 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PHASER | phasing |
| Coot | model building |
| SCALEPACK | data scaling |
| DENZO | data reduction |
