5OOZ
XFEL structure of the on state of a reversibly photoswitching fluorescent protein determined using the grease injection method
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 293.15 | 0.2 M lithium sulfate 0.1 M Tris-Cl pH 8.5 23-30% PEG 3350 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.24 | 45.01 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 39.8 | α = 90 |
| b = 74.6 | β = 90 |
| c = 79.2 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 293.15 | CCD | MPCCD | 2016-05-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL3 | 1.76 | SACLA | BL3 |
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 | 1.911 | 54.3 | 99.74 | 13.77 | 17.7 | 18901 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.92 | 54.3 | 17378 | 927 | 97.69 | 0.15964 | 0.15628 | 0.22863 | RANDOM | 35.383 | |||||||
| 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] | |
| 0.45 | -0.22 | -0.23 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.583 |
| r_long_range_B_refined | 22.731 |
| r_dihedral_angle_4_deg | 22.268 |
| r_dihedral_angle_3_deg | 15.831 |
| r_dihedral_angle_1_deg | 6.876 |
| r_scbond_it | 4.336 |
| r_mcangle_it | 3.118 |
| r_mcbond_it | 2.541 |
| r_angle_refined_deg | 1.957 |
| r_chiral_restr | 0.161 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1743 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 162 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
