3ITP
Crystal structure of Staphylococcal nuclease variant Delta+PHS F34K 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 ID 3BDC, residue 34 truncated to ALA, all water molecules and ligands were removed, All b-factors set to 20A^2, all alternate residue conformations deleted, defaulting to conformation A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | 29%(w/v) MPD, 25 mM Potassium Phosphate, Calcium Chloride (3 M eq), pdTp (2 M eq), 5.5 (mg protein)/mL in stock solution; 4uL protein stock and 4uL well solution per drop; 1-2 weeks of growth, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.027 | α = 90 |
b = 60.296 | β = 92.26 |
c = 38.249 | 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 | Meridionally-bent fused silica mirror with palladium and uncoated stripes | 2009-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 0.97950 | 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 | 1.55 | 40 | 93.9 | 0.046 | 26.9 | 7.3 | 20523 | 19271 |
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) | |||||||||||
1.55 | 1.58 | 60.1 | 0.323 | 3.6 | 606 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ID 3BDC, residue 34 truncated to ALA, all water molecules and ligands were removed, All b-factors set to 20A^2, all alternate residue conformations deleted, defaulting to conformation A | 1.75 | 32.28 | 14283 | 14262 | 749 | 99.85 | 0.205 | 0.204 | 0.203 | 0.235 | RANDOM | 30.152 |
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] | |
-0.05 | 0.03 | -0.04 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.138 |
r_dihedral_angle_3_deg | 13.329 |
r_dihedral_angle_4_deg | 12.152 |
r_scangle_it | 6.371 |
r_dihedral_angle_1_deg | 5.36 |
r_scbond_it | 4.062 |
r_mcangle_it | 2.599 |
r_mcbond_it | 1.526 |
r_angle_refined_deg | 1.215 |
r_chiral_restr | 0.121 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1031 |
Nucleic Acid Atoms | |
Solvent Atoms | 72 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |