Crystal Structure of Oxidized Cypovirus Polyhedra R13A/E73C/Y83C/S193C/A194C Mutant
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | IN CELL | 300 | In vivo crystallization in the cytoplasm of the cell, temperature 300 K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.64 | 24.97 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 103.73 | α = 90 |
| b = 103.73 | β = 90 |
| c = 103.73 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 3 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 9M | 2016-06-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32XU | 1.0 | SPring-8 | BL32XU |
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 | 1.65 | 36.67 | 99.7 | 7.37 | 7 | 20176 | |||||||||||||
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 | 1.65 | 36.67 | 20176 | 2219 | 99.64 | 0.16079 | 0.15647 | 0.17 | 0.20148 | 0.21 | RANDOM | 18.564 | |||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.736 |
| r_dihedral_angle_4_deg | 18.317 |
| r_dihedral_angle_3_deg | 12.982 |
| r_dihedral_angle_1_deg | 6.497 |
| r_long_range_B_refined | 5.759 |
| r_long_range_B_other | 5.731 |
| r_scangle_other | 4.173 |
| r_scbond_it | 2.764 |
| r_scbond_other | 2.758 |
| r_mcangle_it | 2.493 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1912 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 99 |
| Heterogen Atoms | 36 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | phasing |
