7TXR
Crystal structure of the Vitronectin hemopexin-like domain binding Calcium-2
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION containing 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with 1 mM CaCl2, 5 mM SODIUM SULFATE, 27 mM SODIUM NITRATE, 20 mM BisTris pH 7.0, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D-(+)-TREHALOSE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.835 | α = 90 |
b = 98.277 | β = 99.82 |
c = 49.433 | 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 | 2021-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97946 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 37.24 | 92 | 0.112 | 0.84 | 5.6 | 3.3 | 23919 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.05 | 57.6 | 0.51 | 0.72 | 2.6 |
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 | 6o5e | 2 | 37.24 | 22231 | 1667 | 91.85 | 0.1867 | 0.1837 | 0.2259 | RANDOM | 42.023 |
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] | |
0.22 | 0.71 | 0.12 | -0.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.8 |
r_dihedral_angle_4_deg | 15.471 |
r_dihedral_angle_3_deg | 13.173 |
r_dihedral_angle_1_deg | 7.492 |
r_angle_refined_deg | 1.395 |
r_angle_other_deg | 1.194 |
r_chiral_restr | 0.068 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3001 |
Nucleic Acid Atoms | |
Solvent Atoms | 163 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |