2OEO
Cryogenic crystal structure of Staphylococcal Nuclease variant truncated Delta+PHS I92D
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | 20-35% MPD, 10% glycerol, 5% DMSO, 10.5 mM potassium phosphate in the presence of Ca2+ and pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.94 | 36.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30.452 | α = 90 |
b = 57.63 | β = 99.74 |
c = 34.618 | 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 | 95 | IMAGE PLATE | RIGAKU RAXIS IV | mirrors (Osmic) | 2001-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 2 | 20.79 | 100 | 0.042 | 10.1 | 3.4 | 8029 | 8029 | 2 | 1 | 8.1 |
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) | |||||||||||
2 | 2.13 | 100 | 0.136 | 4.4 | 3.4 | 1212 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1SNC | 2 | 20.79 | 8029 | 673 | 100 | 0.1961 | 0.1961 | 0.196 | 0.226 | RANDOM | 10.6 |
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] | |
-1.31 | 2.38 | -0.46 | 1.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.3 |
c_scangle_it | 2.75 |
c_scbond_it | 1.96 |
c_mcangle_it | 1.47 |
c_angle_deg | 1.2 |
c_improper_angle_d | 1.12 |
c_mcbond_it | 1.07 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1019 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
AMoRE | phasing |
CNS | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |