5FB9
S1 nuclease from Aspergillus oryzae with unoccupied active site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 291 | 0.2 M Sodium chloride, 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.5 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 43.184 | ¦Á = 107.37 |
b = 48.595 | ¦Â = 90.13 |
c = 65.469 | ¦Ã = 105.72 |
Symmetry | |
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Space Group | P 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 | PIXEL | DECTRIS PILATUS 6M-F | 2015-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 1.0 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.5 | 43.05 | 88.2 | 0.06 | 9.2 | 1.8 | 68828 | 5.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.5 | 1.53 | 54.6 | 0.187 | 3.8 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | our previous model of S1 | 1.5 | 43.05 | 68827 | 3364 | 88.22 | 0.14963 | 0.14877 | 0.17736 | Random selection | 13.322 |
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] | |
-1.07 | 0.18 | 0.11 | 0.97 | 0.01 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.948 |
r_dihedral_angle_3_deg | 11.398 |
r_dihedral_angle_4_deg | 8.639 |
r_dihedral_angle_1_deg | 5.715 |
r_long_range_B_refined | 4.825 |
r_long_range_B_other | 4.135 |
r_scangle_other | 2.179 |
r_angle_refined_deg | 1.647 |
r_scbond_it | 1.48 |
r_scbond_other | 1.48 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4084 |
Nucleic Acid Atoms | |
Solvent Atoms | 871 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |
Coot | model building |