3DMU
Crystal structure of Staphylococcal nuclease variant PHS T62K at cryogenic temperature
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | 44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.22 | α = 90 |
b = 48.22 | β = 90 |
c = 63.28 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | BRUKER APEX II | multi-layer optics | 2005-01-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OTHER | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.75 | 17.98 | 99.8 | 0.0301 | 0.0199 | 30.16 | 10.6 | 14741 | 14710 | 33.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.75 | 1.84 | 99.3 | 0.2839 | 0.2574 | 4.05 | 3.43 | 2016 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 1EY8.PDB | 1.8 | 17 | 13483 | 12753 | 1272 | 94.61 | 0.23 | 0.203 | 0.198 | 0.255 | RANDOM | 27.909 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.248 |
r_dihedral_angle_4_deg | 20.903 |
r_dihedral_angle_3_deg | 18.093 |
r_dihedral_angle_1_deg | 7.47 |
r_scangle_it | 7.239 |
r_scbond_it | 5.07 |
r_mcangle_it | 3.159 |
r_angle_refined_deg | 2.08 |
r_mcbond_it | 2.056 |
r_chiral_restr | 0.157 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1024 |
Nucleic Acid Atoms | |
Solvent Atoms | 81 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
SAINT | data scaling |
PHASER | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
APEX | data collection |
SAINT | data reduction |