7XXR
Orf1 R342A-glycylthricin complex
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7XQA | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 0.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.37 | 63.46 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 103.42 | α = 90.075 |
| b = 107.933 | β = 90.011 |
| c = 133.424 | γ = 96.303 |
| 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 | 110 | CCD | RAYONIX MX300HE | 2022-02-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSRRC BEAMLINE BL15A1 | 1 | NSRRC | BL15A1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.4 | 30 | 98.5 | 0.06 | 0.069 | 0.033 | 25 | 4.4 | 220494 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.4 | 2.49 | 97.7 | 0.642 | 0.729 | 0.346 | 2.7 | 4.3 | |||||||||||
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 | R-Free | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7XQA | 2.4 | 28.619 | 212738 | 10670 | 94.753 | 0.201 | 0.2004 | 0.2204 | 43.163 | |||||||
| 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] | |
| -0.338 | 0.017 | -0.063 | 0.482 | 0.018 | -0.159 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.295 |
| r_dihedral_angle_3_deg | 17.207 |
| r_dihedral_angle_4_deg | 15.469 |
| r_lrange_other | 8.851 |
| r_lrange_it | 8.849 |
| r_dihedral_angle_1_deg | 6.65 |
| r_scangle_it | 6.645 |
| r_scangle_other | 6.645 |
| r_mcangle_it | 5.341 |
| r_mcangle_other | 5.341 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 29152 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 555 |
| Heterogen Atoms | 664 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
