Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I3 intermediate state.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6G1Z | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 279 | 1.0 - 2.2 M ammonium sulphate, 2 - 12% PEG 1000, 0.1 M HEPES pH 6.8 - 7.7, 0.025% low-melt agarose | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.95 | 68.89 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 184.641 | α = 90 |
| b = 184.641 | β = 90 |
| c = 182.171 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 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 | 298 | CCD | RAYONIX MX170-HS | 2018-05-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.30096 | SLAC LCLS | MFX |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.4 | 26.03 | 99.9 | 0.924 | 31.9 | 533.4 | 68403 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.4 | 2.46 | 0.034 | ||||||||||||||||
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 | 2.4 | 26.03 | 68403 | 1997 | 98.17 | 0.20398 | 0.20348 | 0.2066 | 0.2213 | 0.2202 | RANDOM | 65.749 | |||||
| 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] | |
| -0.55 | -0.27 | -0.55 | 1.78 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 27.597 |
| r_dihedral_angle_4_deg | 17.838 |
| r_dihedral_angle_3_deg | 13.402 |
| r_long_range_B_refined | 6.59 |
| r_long_range_B_other | 6.59 |
| r_dihedral_angle_1_deg | 5.603 |
| r_scangle_other | 4.17 |
| r_mcangle_it | 3.788 |
| r_mcangle_other | 3.788 |
| r_scbond_it | 2.433 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7429 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 115 |
| Heterogen Atoms | 153 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DIALS | data scaling |
| DIALS | data reduction |
| PRIME | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| Coot | model building |
