8BJ5
Imine Reductase IR007 from Amycolatopsis azurea
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.1 | 298 | 0.49 M sodium phosphate; o.91 M potassium phosphate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.65 | 53.62 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.487 | α = 90 |
| b = 142.332 | β = 90 |
| c = 159.931 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | 120 | PIXEL | DECTRIS EIGER2 X 16M | 2021-12-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
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 | 2.72 | 54.1 | 100 | 0.31 | 0.12 | 0.99 | 6.6 | 13.6 | 36218 | 19 | |||||||||
| 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 | 2.72 | 2.84 | 0.98 | 0.38 | 0.95 | 2.3 | |||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6JIZ | 2.72 | 54.1 | 34255 | 1812 | 99.74 | 0.24828 | 0.24688 | 0.27328 | RANDOM | 34.189 | ||||||
| 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] | |
| 0.11 | 7.44 | -7.55 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.191 |
| r_dihedral_angle_3_deg | 19.074 |
| r_dihedral_angle_4_deg | 18.523 |
| r_dihedral_angle_1_deg | 6.622 |
| r_long_range_B_refined | 6.616 |
| r_long_range_B_other | 6.599 |
| r_mcangle_it | 3.928 |
| r_mcangle_other | 3.928 |
| r_scangle_other | 3.703 |
| r_mcbond_it | 2.475 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8539 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 366 |
| Heterogen Atoms | 192 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
