8RUR
High pH (8.0) nitrite-bound MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.38 MGy]
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8RU9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 100 mM Tris pH 7.3, 1.8 M Ammonium Sulphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.92 | α = 90 |
b = 103.92 | β = 90 |
c = 64.25 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2023-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.7749 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.13 | 45.039 | 99.6 | 0.078 | 0.087 | 0.038 | 0.998 | 8.7 | 4.4 | 146809 |
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 | 1.13 | 1.15 | 99.2 | 0.916 | 0.575 | 0.449 | 1.3 | 3.2 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.13 | 45.004 | 146783 | 7537 | 99.629 | 0.117 | 0.1156 | 0.1339 | 15.997 |
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] | |
-0.203 | -0.101 | -0.203 | 0.658 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_other | 20.116 |
r_lrange_it | 20.115 |
r_dihedral_angle_6_deg | 16.401 |
r_dihedral_angle_3_deg | 12.249 |
r_dihedral_angle_2_deg | 11.989 |
r_scangle_it | 9.418 |
r_scangle_other | 9.416 |
r_dihedral_angle_1_deg | 7.955 |
r_scbond_it | 7.308 |
r_scbond_other | 7.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2558 |
Nucleic Acid Atoms | |
Solvent Atoms | 502 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
REFMAC | phasing |