5JQF
Crystal structure of the lasso peptide Sphingopyxin I (SpI)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 291.15 | 0.2 M K2SO4, 20%(w/v) PEG 400 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.59 | 22.43 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 39.24 | α = 90 |
| b = 39.24 | β = 90 |
| c = 31.41 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 |
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 PILATUS 6M-F | 2016-04-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.82656 | ESRF | ID23-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 0.85 | 50 | 99.8 | 0.067 | 0.997 | 12.01 | 5 | 24225 | -3 | 8.602 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 0.85 | 0.9 | 99.6 | 0.689 | 2.2 | ||||||||||||||
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 | AB INITIO PHASING | FREE R-VALUE | 0.85 | 33.98 | 23012 | 1212 | 99.8 | 0.1304 | 0.1292 | 0.153 | RANDOM | 6.914 | |||||||
| 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] | |
| 0.13 | 0.07 | 0.13 | -0.42 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 25.339 |
| r_sphericity_free | 17.628 |
| r_dihedral_angle_3_deg | 10.887 |
| r_dihedral_angle_1_deg | 7.74 |
| r_sphericity_bonded | 4.197 |
| r_rigid_bond_restr | 2.741 |
| r_angle_refined_deg | 1.813 |
| r_angle_other_deg | 1.792 |
| r_mcangle_it | 0.792 |
| r_mcbond_it | 0.608 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 310 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 41 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Coot | model building |
| XDS | data reduction |
| XSCALE | data scaling |
| Sir2014 | phasing |
