6GS3
Crystal Structure of the Uperin-3.5 peptide from Uperoleia mjobergii forming cross-alpha fibril
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Reservoir contained 0.1 M KSCN, 0.1 M MES 6.03 pH, 20 %v/v Jeff 600 with cryo-protection of 20% ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.53 | 19.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 19.7 | α = 90 |
b = 28.44 | β = 106.95 |
c = 20.32 | 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 EIGER R 4M | 2017-04-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9677 | ESRF | MASSIF-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.45 | 19.44 | 97 | 0.085 | 0.089 | 0.999 | 15.7 | 10.636 | 3777 | 21.604 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.45 | 1.49 | 94.7 | 0.601 | 0.648 | 0.908 | 2.72 | 7.568 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | AB INITIO PHASING | THROUGHOUT | 1.45 | 19.44 | 3398 | 378 | 97.24 | 0.189 | 0.185 | 0.2288 | RANDOM | 14.461 |
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] | |
-0.29 | -0.03 | -1.1 | 1.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.735 |
r_dihedral_angle_3_deg | 15.579 |
r_dihedral_angle_4_deg | 6.228 |
r_dihedral_angle_1_deg | 4.162 |
r_angle_refined_deg | 1.783 |
r_angle_other_deg | 0.946 |
r_chiral_restr | 0.103 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 250 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Arcimboldo | phasing |