6FHD
Crystal Structure of the Amyloid-like, out-of-register beta-sheets, polymorph of the LFKFFK segment from the S. aureus PSMalpha3
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 Sodium acetate pH 5.1 , 45 %w/v PEG 400, 0.09 M LiSO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.52 | 18.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.03 | α = 90 |
b = 11.73 | β = 121.89 |
c = 24.61 | 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-F | 2016-05-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.9763 | PETRA III, EMBL c/o DESY | P14 (MX2) |
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 | 1.85 | 19.3 | 96.3 | 0.284 | 0.292 | 0.993 | 9.07 | 17.636 | 913 | 19.453 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.85 | 1.96 | 91.9 | 0.547 | 0.563 | 0.946 | 5.61 | 17.5 |
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 | Ideal beta-strand of poly-alanine | 1.85 | 19.3 | 821 | 92 | 97.33 | 0.1728 | 0.1712 | 0.1869 | RANDOM | 11.819 |
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] | |
1.19 | 0.02 | -0.53 | -0.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.695 |
r_dihedral_angle_3_deg | 17.116 |
r_dihedral_angle_1_deg | 8.292 |
r_angle_other_deg | 2.508 |
r_angle_refined_deg | 1.893 |
r_chiral_restr | 0.097 |
r_bond_other_d | 0.035 |
r_gen_planes_other | 0.019 |
r_bond_refined_d | 0.017 |
r_gen_planes_refined | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 120 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |