3D6C
Crystal structure of Staphylococcal nuclease variant PHS L38E at cryogenic temperature
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 35% MPD, 25 mM Potassium Phosphate, Calcium chloride, PTP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.256 | α = 90 |
b = 48.256 | β = 90 |
c = 62.675 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
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 | APEX II | multi-layer optics | 2007-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER | 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 | 2 | 48.3 | 99.8 | 0.0216 | 0.0431 | 40.02 | 13.82 | 9801 | 9781 | 25.6 |
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) | ||||||||||
2 | 2.1 | 98.9 | 0.1097 | 0.1807 | 8.31 | 5.88 | 1323 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 2 | 48.28 | 1 | 9781 | 9740 | 971 | 99.64 | 0.197 | 0.179 | 0.173 | 0.234 | RANDOM | 17.646 |
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 | 32.54 |
r_dihedral_angle_3_deg | 13.887 |
r_dihedral_angle_4_deg | 10.056 |
r_dihedral_angle_1_deg | 5.902 |
r_scangle_it | 3.616 |
r_scbond_it | 2.552 |
r_angle_refined_deg | 1.591 |
r_mcangle_it | 1.482 |
r_mcbond_it | 1.102 |
r_nbtor_refined | 0.298 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1077 |
Nucleic Acid Atoms | |
Solvent Atoms | 93 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
APEX | data collection |
SAINT | data reduction |
SAINT | data scaling |