6PFZ
Structure of a NAD-Dependent Persulfide Reductase from A. fulgidus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 100-200 mM calcium acetate, 15-20% PEG 3350 (w/w), and 1 mM DTT |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 48.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.976 | α = 90 |
b = 100.355 | β = 91.894 |
c = 136.196 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | ADSC QUANTUM 315 | Cryogenically-cooled single crystal Si(220) side bounce monochromator. | 2016-05-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.98 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 3.1 | 40 | 99.7 | 0.119 | 10.3 | 5.2 | 80127 | 2 | 2 | 58.5513273334 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.1 | 3.27 | 0.54 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4FX9 | 3.10003870577 | 39.4818037712 | 1.06887880485 | 79880 | 2782 | 97.8645724857 | 0.203188436559 | 0.202274311858 | 0.228746674435 | 55.5125936023 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 24.6929780096 |
f_angle_d | 1.98726418669 |
f_chiral_restr | 0.292776968012 |
f_bond_d | 0.0239630998156 |
f_plane_restr | 0.0119689849829 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16658 |
Nucleic Acid Atoms | |
Solvent Atoms | 14 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
BALBES | phasing |