8RKE
Crystal structure of the complete N-terminal region of human ZP2 (hZP2-N1N2N3)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 277 | 10% (w/v) PEG 4000, 0.1 M MES/imidazole pH 6.5, 0.1 M carboxylic acids (MD2-100-76, Molecular Dimensions), 20% (v/v) glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.32 | 63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 147.68 | α = 90 |
b = 97.77 | β = 94.803 |
c = 104.33 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 2019-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91840 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.7 | 21.92 | 99.2 | 0.082 | 0.089 | 0.034 | 1 | 15.7 | 6.9 | 40494 | 79.73 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.7 | 2.8 | 98 | 2.152 | 2.345 | 0.916 | 0.51 | 0.9 | 6.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SIRAS | FREE R-VALUE | 2.7 | 21.92 | 1.34 | 40446 | 1575 | 99.42 | 0.2297 | 0.2286 | 0.2578 | 117.85 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 10.5438 |
f_angle_d | 0.7752 |
f_chiral_restr | 0.0543 |
f_plane_restr | 0.0068 |
f_bond_d | 0.0042 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6616 |
Nucleic Acid Atoms | |
Solvent Atoms | 31 |
Heterogen Atoms | 239 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
SHARP | phasing |
PHENIX | model building |
Coot | model building |
PHENIX | refinement |