X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6ZQ9 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyehylene glycol 8000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 38.42 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 20.97 | α = 105.839 |
| b = 26.43 | β = 96.657 |
| c = 38.68 | γ = 92.025 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
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 | 2018-12-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 1.283 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.52 | 37 | 88.2 | 0.069 | 0.081 | 0.998 | 9.49 | 3.55 | 10765 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.52 | 1.61 | 74.1 | 0.566 | 0.664 | 0.889 | 1.78 | 3.5 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6ZQ9 | 1.52 | 36.893 | 10761 | 567 | 88.321 | 0.19 | 0.1874 | 0.2 | 0.2352 | 0.24 | 16.865 | |||||
| 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] | |
| -0.312 | 0.435 | -0.357 | 1.633 | -0.462 | -0.823 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_lrange_it | 4.779 |
| r_lrange_other | 3.948 |
| r_angle_refined_deg | 1.746 |
| r_scangle_it | 1.691 |
| r_scangle_other | 1.69 |
| r_scbond_it | 1.288 |
| r_scbond_other | 1.286 |
| r_angle_other_deg | 1.266 |
| r_symmetry_nbd_other | 0.277 |
| r_xyhbond_nbd_refined | 0.263 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 676 |
| Solvent Atoms | 181 |
| Heterogen Atoms | 7 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
