8BD0
Human Gamma-D crystallin R36S mutant with DTT-Cystein Protein modification
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 7.8 | 298 | 50 mM phosphate buffer pH 7.8, 20 mM DTT |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.8 | 56.07 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 53.9 | α = 90 |
| b = 83.7 | β = 90 |
| c = 101 | 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 | 298 | PIXEL | DECTRIS EIGER X 1M | 2019-12-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.98 | PETRA III, EMBL c/o DESY | P14 (MX2) |
Serial Crystallography
| Sample delivery method | ||
|---|---|---|
| Diffraction ID | Description | Sample Delivery Method |
| 1 | fixed target | |
| Data Reduction | |||
|---|---|---|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
| 1 | 25600 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | 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 | 101.13 | 99.99 | 0.9956 | 0.2717 | 2.71 | 50.3 | 31629 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2 | 2.07 | 100 | 0.14 | 1.94 | 0.6 | 34.7 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 2G98 | 2 | 101 | 25054 | 1718 | 84.79 | 0.20727 | 0.20437 | 0.24971 | RANDOM | 35.637 | ||||||
| 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] | |
| -0.43 | 0.26 | 0.17 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.078 |
| r_dihedral_angle_4_deg | 19.74 |
| r_dihedral_angle_3_deg | 16.778 |
| r_long_range_B_other | 9.318 |
| r_long_range_B_refined | 9.317 |
| r_dihedral_angle_1_deg | 7.207 |
| r_scangle_other | 6.041 |
| r_scbond_it | 3.887 |
| r_scbond_other | 3.886 |
| r_mcangle_other | 3.447 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2858 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 81 |
| Heterogen Atoms | 32 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| MOLREP | phasing |
