9FIF
Crystal Structure of NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6HL2 | Chains A and B were placed independently two times in the asymmetric unit |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.3 | 281 | 0.1 M BisTris pH 6.3, 1.6 M ammonium sulfate, 150 mM NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.399 | α = 90 |
b = 116.035 | β = 90 |
c = 189.72 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2020-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.9724 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.77 | 48.037 | 100 | 0.047 | 0.997 | 9.2 | 6.2 | 136928 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.77 | 1.8 | 0.487 | 0.721 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.77 | 48.037 | 136826 | 6886 | 99.935 | 0.165 | 0.1633 | 0.1886 | Random selection | 27.176 |
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] | |
0.745 | 0.533 | -1.278 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 14.61 |
r_dihedral_angle_other_3_deg | 13.803 |
r_dihedral_angle_3_deg | 11.475 |
r_dihedral_angle_2_deg | 6.719 |
r_dihedral_angle_1_deg | 6.051 |
r_lrange_it | 5.335 |
r_lrange_other | 5.105 |
r_scangle_it | 2.822 |
r_scangle_other | 2.771 |
r_scbond_it | 1.746 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9125 |
Nucleic Acid Atoms | |
Solvent Atoms | 992 |
Heterogen Atoms | 172 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |