3NK9
Crystal structure of Staphylococcal nuclease variant Delta+PHS V74A 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 | 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, V74A, T82A, Y113A, V114A and Y115A; all b-factors were reset to 20 A^2. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | 22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.075 | α = 90 |
b = 60.435 | β = 93.3 |
c = 38.129 | 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 | 100 | CCD | ADSC QUANTUM 315 | 2010-01-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.1000 | NSLS | X25 |
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 | 1.65 | 50 | 98.8 | 0.046 | 22.3 | 7.2 | 16836 | 16836 |
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 | 1.65 | 1.68 | 96 | 0.183 | 6.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, V74A, T82A, Y113A, V114A and Y115A; all b-factors were reset to 20 A^2. | 1.65 | 30.22 | 16991 | 15112 | 1677 | 98.78 | 0.1855 | 0.18132 | 0.2243 | RANDOM | 27.894 |
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] | |
-1.9 | 0.85 | -1.69 | 3.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.666 |
r_dihedral_angle_3_deg | 15.413 |
r_dihedral_angle_4_deg | 12.275 |
r_dihedral_angle_1_deg | 6.418 |
r_scangle_it | 4.398 |
r_scbond_it | 3.039 |
r_mcangle_it | 1.915 |
r_angle_refined_deg | 1.611 |
r_mcbond_it | 1.318 |
r_chiral_restr | 0.123 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1031 |
Nucleic Acid Atoms | |
Solvent Atoms | 76 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
HKL-2000 | data reduction |