X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8WGG | PilB protein |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 295 | 0.1 M HEPES pH 7.5, 0.01 M Cadmium Sulphate, 1.0 M Sodium acetate tri-hydrate. | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.01 | 59.19 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 60.593 | α = 90 |
| b = 89.949 | β = 90 |
| c = 216.408 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 2 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2023-04-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.8856 | ESRF | ID23-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.995 | 58.35 | 87.8 | 0.094 | 0.054 | 0.989 | 7.8 | 3.8 | 36257 | 29.2 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.995 | 2.159 | 90.5 | 0.543 | 0.379 | 0.592 | 2.8 | ||||||||||||
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 | 1.995 | 58.35 | 34403 | 1854 | 87.8 | 0.21184 | 0.2093 | 0.2163 | 0.25936 | 0.2632 | RANDOM | 32.359 | |||||
| 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] | |
| -0.47 | 0.33 | 0.14 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.407 |
| r_dihedral_angle_4_deg | 18.856 |
| r_dihedral_angle_3_deg | 14.564 |
| r_dihedral_angle_1_deg | 8.088 |
| r_long_range_B_refined | 6.415 |
| r_long_range_B_other | 6.415 |
| r_scangle_other | 3.211 |
| r_mcangle_it | 3.096 |
| r_mcangle_other | 3.096 |
| r_angle_other_deg | 2.811 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6412 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 34 |
| Heterogen Atoms | 29 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| PHASER | phasing |
| Coot | model building |
| REFMAC | refinement |
| Aimless | data scaling |
