5JOB
Crystal structure of Staphylococcal nuclease variant Delta+PHS L25K/I92A at cryogenic temperature
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | 30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.136 | α = 90 |
b = 60.5 | β = 94.01 |
c = 38.149 | 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 | PIXEL | DECTRIS PILATUS 6M | 2011-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.00 | 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 | 1.25 | 50 | 98.5 | 0.048 | 70.691 | 11.4 | 25088 | 25080 | 19.62 |
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 | 1.25 | 1.27 | 84.6 | 0.342 | 3.585 | 5.7 |
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 | 1.45 | 38.06 | 23774 | 1306 | 99.97 | 0.1586 | 0.1574 | 0.1817 | RANDOM | 21.622 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.49 | -0.09 | -1.22 | 1.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.477 |
r_rigid_bond_restr | 17.127 |
r_dihedral_angle_3_deg | 13.37 |
r_sphericity_free | 12.697 |
r_dihedral_angle_4_deg | 9.011 |
r_dihedral_angle_1_deg | 6.519 |
r_sphericity_bonded | 5.584 |
r_scbond_it | 2.343 |
r_mcangle_it | 1.641 |
r_angle_refined_deg | 1.502 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1027 |
Nucleic Acid Atoms | |
Solvent Atoms | 118 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
Coot | model building |