8QQ1
SpNOX dehydrogenase domain, mutant F397W in complex with Flavin adenine dinucleotide (FAD)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Crystals Obtained at the HTX Facility, EMBL Grenoble 17% w/v PEG3350, 0.1M BIS-TRIS Propane pH6.5, 0.2M Sodium bromide. Automatic harvesting and cryocooling with CrystalDirect |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.622 | α = 90 |
b = 104.622 | β = 90 |
c = 142.688 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 PILATUS 6M | Vertical CRL / Horizontal elliptical mirror | 2018-09-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.9184 | ESRF | ID30B |
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 | 1.941 | 58.944 | 98.4 | 0.117 | 0.119 | 0.023 | 0.998 | 21.2 | 13.8 | 57719 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.941 | 1.974 | 95.6 | 1.829 | 0.372 | 0.723 | 2.1 | 12.9 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.941 | 36.99 | 57709 | 2885 | 97.6 | 0.1919 | 0.1902 | 0.2249 | RANDOM | 38.64 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.3933 | -0.3933 | 0.7865 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.82 |
t_omega_torsion | 3.51 |
t_angle_deg | 0.91 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5304 |
Nucleic Acid Atoms | |
Solvent Atoms | 548 |
Heterogen Atoms | 185 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
MxCuBE | data collection |
CRANK2 | phasing |
Aimless | data scaling |
autoPROC | data processing |
Coot | model building |
XDS | data reduction |