4PNY
Crystal structure of Staphylococcal nuclease variant Delta+PHS I72H 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 | 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.172 | α = 90 |
b = 60.573 | β = 93.79 |
c = 37.442 | 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 | 110 | CCD | BRUKER APEX | multi-layer optics | 2013-06-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OTHER | 1.54 |
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 | 1.68 | 50 | 99.9 | 0.0301 | 20.59 | 8 | 15921 | 15921 | 25.2 |
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 | 1.68 | 1.71 | 100 | 0.2093 | 4.35 | 5.21 | 557 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 3BDC | 1.68 | 31.8 | 15882 | 15882 | 791 | 99.82 | 0.1975 | 0.1975 | 0.1954 | 0.2417 | RANDOM | 23.54 |
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] | |
-0.06 | 0.16 | -0.94 | 0.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.101 |
r_dihedral_angle_3_deg | 15.368 |
r_dihedral_angle_4_deg | 9.456 |
r_dihedral_angle_1_deg | 6.6 |
r_angle_refined_deg | 1.904 |
r_angle_other_deg | 0.842 |
r_chiral_restr | 0.122 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1044 |
Nucleic Acid Atoms | |
Solvent Atoms | 86 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
SAINT | data reduction |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
APEX | data collection |
SAINT | data scaling |