8Q1V
TtX183A - A c-type cytochrome domain from the Teredinibacter turnerae protein TERTU_2913
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 291 | 20-25 % (w/v) PEG 6000, 1 M LiCl2 and 0.1 M Citrate pH 4.0 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.35 | 63.27 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 92.669 | α = 90 |
| b = 92.669 | β = 90 |
| c = 92.669 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 3 2 |
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 PILATUS3 2M | 2017-11-29 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-1 |
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 | 1.4 | 65.53 | 100 | 0.125 | 0.129 | 0.029 | 1 | 22.5 | 36.9 | 27430 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.4 | 1.42 | 3.874 | 3.976 | 0.894 | 0.629 | 37.5 | ||||||||||||
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 | R-Free | Mean Isotropic B | ||||||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.4 | 65.53 | 27351 | 1355 | 99.923 | 0.166 | 0.1645 | 0.193 | 19.5 | ||||||||
| 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_6_deg | 15.718 |
| r_dihedral_angle_3_deg | 15.241 |
| r_dihedral_angle_2_deg | 13.337 |
| r_lrange_it | 12.77 |
| r_lrange_other | 11.932 |
| r_scangle_it | 8.016 |
| r_scangle_other | 8.008 |
| r_mcangle_other | 6.895 |
| r_mcangle_it | 6.88 |
| r_dihedral_angle_1_deg | 5.855 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 561 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 60 |
| Heterogen Atoms | 46 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| REFMAC | refinement |
| Aimless | data scaling |
| SHELX | phasing |
| XDS | data reduction |
