5F2D
Crystal structure of Staphylococcal nuclease variant Delta+PHS I92N/V99T at cryogenic temperature
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BDC | PDB entry 3BDC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 277 | 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.118 | α = 90 |
b = 60.503 | β = 93.28 |
c = 38.184 | 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 | APEX II CCD | mirrors | 2014-03-13 | 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 | 1.7 | 50 | 100 | 0.0139 | 48.29 | 25.14 | 15639 | 15639 | 22.76 |
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 | 1.7 | 1.72 | 100 | 0.1118 | 6.73 | 8.74 |
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 | PDB entry 3BDC | 1.7 | 38.12 | 14776 | 778 | 99.55 | 0.1917 | 0.1901 | 0.2216 | RANDOM | 18.431 |
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] | |
-1.13 | 0.36 | -1.3 | 2.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.262 |
r_dihedral_angle_3_deg | 17.774 |
r_dihedral_angle_4_deg | 8.918 |
r_dihedral_angle_1_deg | 6.353 |
r_angle_refined_deg | 1.836 |
r_mcangle_it | 1.719 |
r_scbond_it | 1.525 |
r_mcbond_it | 1.124 |
r_chiral_restr | 0.144 |
r_gen_planes_refined | 0.017 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1033 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
APEX 2 | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
APEX 2 | data reduction |
Coot | model building |