6GT0
Nitrite-bound copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293.15 | 1.2 M ammonium sulphate, 100 mM citrate buffer, pH 5.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.96 | 37.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.92 | α = 90 |
b = 94.92 | β = 90 |
c = 94.92 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 | CCD | RAYONIX MX225-HS | 2017-10-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.242 | SACLA | BL2 |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | fixed target |
Fixed Target | ||||||
---|---|---|---|---|---|---|
Diffraction ID | Description | Sample Holding | Support Base | Motion control | Sample Solvent | |
1 | Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) | Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) | SACLA goniometer | 3.4 M Na-malonate, pH 5.0 and 100 mM NaNO2. |
Measurement | |||||
---|---|---|---|---|---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 10 | 30 |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 1039 | 1257 | 1257 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Split (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 | 1.5 | 54.86 | 100 | 0.106 | 6.6 | 154.7 | 45846 | 22.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.5 | 1.54 | 100 | 0.853 | 2.3 | 50.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | THROUGHOUT | 1.5 | 54.86 | 43498 | 2295 | 99.99 | 0.14481 | 0.14343 | 0.17053 | RANDOM | 19.23 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.831 |
r_dihedral_angle_4_deg | 21.782 |
r_dihedral_angle_1_deg | 21.215 |
r_dihedral_angle_3_deg | 12.809 |
r_long_range_B_refined | 4.666 |
r_long_range_B_other | 4.323 |
r_scangle_other | 3.584 |
r_scbond_it | 2.524 |
r_scbond_other | 2.472 |
r_mcangle_it | 1.852 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2574 |
Nucleic Acid Atoms | |
Solvent Atoms | 395 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
CrystFEL | data reduction |
REFMAC | refinement |