7BKX
Diploptera punctata inspired lipocalin-like Milk protein expressed in Saccharomyces cerevisiae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 15% of PEG MME 550, 100 mM MES pH 6.5, and 10 mM ZnSO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.36 | 63.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.61 | α = 90 |
b = 135.662 | β = 90 |
c = 39.654 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 2019-04-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.9786 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 2.35 | 20.612 | 100 | 0.073 | 0.998 | 18.1 | 12.7 | 12200 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.35 | 2.39 | 0.836 | 0.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4NYQ | 2.35 | 20.6 | 12161 | 573 | 99.77 | 0.225 | 0.2222 | 0.2782 | 58.393 |
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] | |
-2.572 | 1.942 | 0.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.272 |
r_dihedral_angle_4_deg | 25.394 |
r_dihedral_angle_3_deg | 18.236 |
r_dihedral_angle_1_deg | 11.401 |
r_lrange_it | 8.876 |
r_lrange_other | 8.864 |
r_scangle_it | 5.767 |
r_scangle_other | 5.764 |
r_mcangle_it | 4.793 |
r_mcangle_other | 4.79 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1234 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 97 |
Software
Software | |
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Software Name | Purpose |
xia2 | data reduction |
Aimless | data scaling |
PHASER | phasing |
PHENIX | refinement |
Coot | model building |