Low pH (5.5) as-isolated MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.71 MGy]
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8R8S | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 50 mM Hepes pH 5.5, 1.8 M Ammonium Sulphate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.52 | 51.17 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 103.99 | α = 90 |
| b = 103.99 | β = 90 |
| c = 64.57 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 |
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-F | 2022-07-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.855 | Diamond | I24 |
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 | 1.17 | 52.48 | 99.1 | 0.057 | 0.071 | 0.04 | 0.998 | 9.2 | 4.3 | 132306 | |||||||||
| 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 | 1.17 | 1.19 | 1.698 | 2.092 | 1.191 | 0.327 | 3.8 | ||||||||||||
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.17 | 52.049 | 132275 | 6668 | 99.017 | 0.119 | 0.1177 | 0.11 | 0.1421 | 0.14 | 18.505 | ||||||
| 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] | |
| -0.337 | -0.168 | -0.337 | 1.093 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_lrange_it | 18.293 |
| r_lrange_other | 18.291 |
| r_dihedral_angle_6_deg | 15.695 |
| r_dihedral_angle_3_deg | 11.505 |
| r_dihedral_angle_2_deg | 11.441 |
| r_scangle_it | 9.538 |
| r_scangle_other | 9.536 |
| r_dihedral_angle_1_deg | 7.676 |
| r_scbond_it | 7.254 |
| r_scbond_other | 7.252 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2553 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 505 |
| Heterogen Atoms | 45 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| REFMAC | refinement |
| xia2 | data reduction |
| Aimless | data scaling |
| REFMAC | phasing |
