6XSH
Crystal structure of Staphylococcal nuclease variant Delta+PHS T62V 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 | 6 | 277 | 20% MPD, 25 mM potassium phosphate, calcium chloride, THP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.062 | α = 90 |
b = 60.717 | β = 94.04 |
c = 38.119 | 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 | AGILENT ATLAS CCD | 2018-03-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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 | 2 | 38.02 | 99.9 | 0.045 | 47.52 | 10.7 | 9637 | 33.5 |
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 | 2 | 2.07 | 100 | 0.247 | 5.61 | 7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2 | 38.02 | 9167 | 456 | 99.94 | 0.2348 | 0.2327 | 0.2757 | RANDOM | 35.777 |
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] | |
0.04 | -0.03 | -0.04 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.974 |
r_dihedral_angle_3_deg | 17.869 |
r_dihedral_angle_4_deg | 15.583 |
r_dihedral_angle_1_deg | 6.344 |
r_angle_refined_deg | 1.652 |
r_angle_other_deg | 0.772 |
r_chiral_restr | 0.078 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1033 |
Nucleic Acid Atoms | |
Solvent Atoms | 31 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrysalisPro | data reduction |
CrysalisPro | data scaling |
REFMAC | model building |