X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9IOK | Sortase E wild type |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 295 | 1.5M Lithium sulfate, 0.1M HEPES-NaOH, pH 7.5 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.91 | 57.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 111.939 | α = 90 |
| b = 111.939 | β = 90 |
| c = 71.638 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 |
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 EIGER2 S 16M | 2023-04-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.885603 | ESRF | ID23-1 |
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 | 1.5 | 41.03 | 92.8 | 0.067 | 0.075 | 0.034 | 0.996 | 9.4 | 4.5 | 48207 | |||||||||
| 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 | 1.5 | 1.57 | 80.7 | 0.456 | 0.509 | 0.223 | 0.807 | 1.8 | 5.1 | ||||||||||
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 | 1.5 | 41.03 | 45710 | 2495 | 68.33 | 0.14556 | 0.1437 | 0.1438 | 0.17905 | 0.1793 | RANDOM | 18.822 | |||||
| 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] | |
| 0.19 | 0.19 | -0.38 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 12.634 |
| r_long_range_B_other | 12.397 |
| r_dihedral_angle_3_deg | 11.114 |
| r_scangle_other | 10.074 |
| r_mcangle_it | 6.968 |
| r_mcangle_other | 6.967 |
| r_scbond_it | 6.935 |
| r_scbond_other | 6.935 |
| r_dihedral_angle_1_deg | 6.748 |
| r_mcbond_it | 4.651 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2712 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 267 |
| Heterogen Atoms | 27 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| autoPROC | data reduction |
| autoPROC | data scaling |
| PHASER | phasing |
