6P5G
Photoactive Yellow Protein PYP Dark Full
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 293 | Sodium Malonate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.88 | 34.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.9 | α = 90 |
b = 66.9 | β = 90 |
c = 40.8 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | 300 | PIXEL | AGIPD | 2019-03-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | EUROPEAN XFEL BEAMLINE SPB/SFX | 1.3 | European XFEL | SPB/SFX |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.6 | 33.45 | 95.57 | 13.65 | 280.8 | 12625 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.6 | 1.642 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.6 | 33.45 | 12625 | 632 | 95.57 | 0.16608 | 0.16439 | 0.2012 | RANDOM | 14.359 |
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] | |
-0.09 | -0.05 | -0.09 | 0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 6.463 |
r_long_range_B_other | 6.137 |
r_scangle_other | 4.483 |
r_scbond_it | 2.85 |
r_scbond_other | 2.85 |
r_mcangle_it | 2.418 |
r_mcangle_other | 2.417 |
r_angle_refined_deg | 1.874 |
r_mcbond_it | 1.575 |
r_mcbond_other | 1.573 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 987 |
Nucleic Acid Atoms | |
Solvent Atoms | 92 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHENIX | phasing |