X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | protein 10-11 mg/ml, 20 mM HEPES pH 8, 200 mM NaCl. reservoir 100 mM imidazole pH 6.5, 1.5 M NaCl, 15 % w/v PEG 3350, 100 mM MgCl2. Cryoprotection Parabar 10312 (Hampton Research) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.29 | 46.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 49 | α = 90 |
| b = 49 | β = 90 |
| c = 116.241 | 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 | 273 | PIXEL | DECTRIS PILATUS 2M | 2019-07-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.45883 | LNLS | W01B-MX2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.47 | 42.44 | 96.1 | 0.041 | 0.042 | 1 | 25.9 | 16 | 27246 | 38.28 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.47 | 1.56 | 76.1 | 0.297 | 0.317 | 0.292 | 0.56 | 7.5 | |||||||||||
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | AB INITIO PHASING | FREE R-VALUE | 1.471 | 42.435 | 27246 | 2036 | 96.262 | 0.219 | 0.2168 | 0.22 | 0.2445 | 0.24 | 39.496 | ||||||
| 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] | |
| 0.658 | 0.329 | 0.658 | -2.133 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.244 |
| r_dihedral_angle_4_deg | 19.598 |
| r_dihedral_angle_3_deg | 12.028 |
| r_dihedral_angle_1_deg | 6.701 |
| r_lrange_it | 5.885 |
| r_lrange_other | 5.87 |
| r_scangle_it | 2.838 |
| r_scangle_other | 2.837 |
| r_scbond_it | 1.885 |
| r_scbond_other | 1.883 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1178 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 66 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| Arcimboldo | phasing |
