9FEA
Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NAD+
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 used as ensemble that was placed two times independently in the asymmetric unit |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 281 | 100 mM BisTris pH 6.5, 1.6 M ammonium sulfate, 150 mM NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.582 | α = 90 |
b = 115.785 | β = 90 |
c = 190.011 | 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 | |||||
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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 | 1.66 | 49.486 | 97.2 | 0.064 | 0.993 | 6.9 | 4 | 161000 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.66 | 1.69 | 0.506 | 0.62 |
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 | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.66 | 49.486 | 160798 | 7928 | 96.865 | 0.174 | 0.1729 | 0.1963 | Random selection | 22.061 |
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] | |
0.196 | 0.732 | -0.928 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 15.093 |
r_dihedral_angle_other_3_deg | 14.795 |
r_dihedral_angle_3_deg | 11.391 |
r_dihedral_angle_2_deg | 7.829 |
r_lrange_it | 6.046 |
r_dihedral_angle_1_deg | 6.031 |
r_lrange_other | 5.876 |
r_scangle_it | 2.56 |
r_scangle_other | 2.487 |
r_scbond_it | 1.614 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9138 |
Nucleic Acid Atoms | |
Solvent Atoms | 1156 |
Heterogen Atoms | 211 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |