ATP-dependent Clp endopeptidase proteolytic subunit ClpP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 291 | 0.2 M ammonium acetate, 0.1 M tris pH 8.0, PEG 10000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.27 | 62.34 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 252.981 | α = 90 |
| b = 273.576 | β = 90 |
| c = 249.499 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 | 2024-09-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.97918 | SSRF | BL02U1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.03 | 32.73 | 99.9 | 0.997 | 10 | 13.5 | 166729 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 3.03 | 3.11 | 0.813 | ||||||||||||||||
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 | 3.03 | 32.73 | 157723 | 8375 | 99.45 | 0.2167 | 0.21502 | 0.2173 | 0.2481 | 0.2496 | RANDOM | 75.894 | |||||
| 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] | |
| 2.93 | -6.91 | 3.97 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.733 |
| r_dihedral_angle_4_deg | 20.146 |
| r_dihedral_angle_3_deg | 15.816 |
| r_long_range_B_other | 14.084 |
| r_long_range_B_refined | 14.082 |
| r_scangle_other | 10.016 |
| r_mcangle_it | 8.899 |
| r_mcangle_other | 8.898 |
| r_scbond_it | 6.529 |
| r_scbond_other | 6.529 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 39874 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 635 |
| Heterogen Atoms | 252 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
