4TRD
Crystal structure of Staphylcoccal nuclease variant Delta+PHS I72K/V74K at pH 9.0 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, 25mM potassium phosphate, calcium chloride, pdTp |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.809 | α = 90 |
b = 60.204 | β = 90 |
c = 73.827 | 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 | CCD | APEX II CCD | mirrors | 2014-04-28 | 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 | 1.6 | 50 | 100 | 0.0237 | 33.96 | 18.49 | 19443 | 19443 | 19.7 |
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 | 1.6 | 1.62 | 100 | 0.1827 | 5.09 | 5.73 |
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 | 1.6 | 31.47 | 19388 | 991 | 99.97 | 0.1713 | 0.17 | 0.1947 | RANDOM | 13.591 |
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] | |
-0.07 | 0.22 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.975 |
r_dihedral_angle_3_deg | 15.325 |
r_dihedral_angle_4_deg | 13.299 |
r_dihedral_angle_1_deg | 6.879 |
r_angle_refined_deg | 1.863 |
r_angle_other_deg | 1.131 |
r_chiral_restr | 0.112 |
r_bond_refined_d | 0.017 |
r_gen_planes_refined | 0.013 |
r_gen_planes_other | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1053 |
Nucleic Acid Atoms | |
Solvent Atoms | 131 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
SAINT | data reduction |
PDB_EXTRACT | data extraction |
PHASER | phasing |
REFMAC | refinement |