Crystal Structure of anti-CRISPR AcrIE7 Determined by Experimental MAD Phasing with Hg
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 1.5M Na Malonate (pH 8.0), 0.1M HEPES (pH 7.5) Crystals soaked in Mother Liquor containing 1mM HgCl2 overnight before backsoaking in cryoprotectant (2.6M Na Malonate) and plunge freezing |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.39 | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 108.102 | α = 90 |
| b = 108.102 | β = 90 |
| c = 187.713 | 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 | 90 | PIXEL | DECTRIS EIGER X 16M | 2023-04-23 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.9753, 1.0070, 1.0088, 1.0108 | APS | 23-ID-B |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.198 | 49.95 | 99.9 | 0.334 | 0.342 | 0.073 | 0.998 | 15.3 | 39.8 | 33732 | 16.28 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.2 | 2.33 | 99.4 | 1.63 | 0.79 | 2.19 | |||||||||||||
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 | MAD | FREE R-VALUE | 2.198 | 46.928 | 33731 | 1784 | 99.825 | 0.193 | 0.1907 | 0.1927 | 0.2268 | 0.228 | 29.175 | ||||||
| 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] | |
| 0.421 | 0.21 | 0.421 | -1.365 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_6_deg | 16.598 |
| r_dihedral_angle_3_deg | 15.704 |
| r_dihedral_angle_2_deg | 14.849 |
| r_lrange_other | 6.316 |
| r_lrange_it | 6.307 |
| r_dihedral_angle_1_deg | 5.831 |
| r_scangle_it | 4.795 |
| r_scangle_other | 4.793 |
| r_scbond_it | 3.188 |
| r_scbond_other | 3.132 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2524 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 352 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| pointless | data scaling |
| SHELXCD | phasing |
| SHELXDE | phasing |
| Blu-Ice | data collection |
| Coot | model building |
