5FBF
S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 3.8 | 291 | 0.1 M Citric acid pH 3.8, 25% w/v Polyethylene glycol 3,350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.81 | 32.3 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 53.742 | ¦Á = 90 |
b = 62.388 | ¦Â = 90 |
c = 62.762 | ¦Ã = 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 | 2014-04-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91842 | BESSY | 14.1 |
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 | 1.04 | 44.25 | 94.5 | 0.089 | 10.7 | 6 | 96234 | 4.8 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.04 | 1.06 | 54.5 | 0.307 | 2.7 | 2.3 |
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 | 1.04 | 44.25 | 96142 | 4712 | 94.46 | 0.11315 | 0.11106 | 0.13509 | Random selection | 8.324 |
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] | |
-0.54 | 0.32 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.967 |
r_sphericity_free | 21.937 |
r_dihedral_angle_4_deg | 11.661 |
r_dihedral_angle_3_deg | 11.187 |
r_rigid_bond_restr | 8.247 |
r_dihedral_angle_1_deg | 5.948 |
r_sphericity_bonded | 5.778 |
r_long_range_B_refined | 2.764 |
r_angle_other_deg | 2.067 |
r_long_range_B_other | 1.992 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2049 |
Nucleic Acid Atoms | |
Solvent Atoms | 485 |
Heterogen Atoms | 72 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |
Coot | model building |