9C11
Crystal structure of Staphylococcal nuclease variant Delta+PHS L36R 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 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | 28% MPD 25mM K Phosphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.183 | α = 90 |
b = 53.201 | β = 90 |
c = 107.422 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | RIGAKU HyPix-6000HE | 2023-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU PhotonJet-R | 1.54184 |
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 | 1.95 | 23.21 | 99.8 | 0.015 | 0.043 | 104.39 | 9.6 | 22934 | 25.76 |
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 | 1.95 | 2.02 | 99.9 | 0.193 | 0.242 | 5.88 | 7.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.95 | 21.76 | 21748 | 1137 | 99.86 | 0.21313 | 0.21065 | 0.26094 | RANDOM | 43.065 |
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] | |
-1.19 | 0.31 | 0.88 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 15.514 |
r_dihedral_angle_3_deg | 13.61 |
r_long_range_B_refined | 7.752 |
r_long_range_B_other | 7.712 |
r_dihedral_angle_1_deg | 6.097 |
r_scangle_other | 5.345 |
r_mcangle_it | 3.456 |
r_mcangle_other | 3.455 |
r_scbond_it | 3.334 |
r_scbond_other | 3.333 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2174 |
Nucleic Acid Atoms | |
Solvent Atoms | 163 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data scaling |
CrysalisPro | data reduction |
PHASER | phasing |