5O3U
Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | PCY1-S562A complex with PresegF1 was crystallized at 13.0 mg/mL with 0.161.3 mM PresegB1 in 27% (w/v) PEG 3350, 100 mM Ca chloride and 0.1 M Bis-Tris at pH 6.5. For cryo protection 10 % (v/v) glycerol were added to reservoir solution. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.86 | α = 87.64 |
b = 85.82 | β = 78.32 |
c = 137.87 | γ = 89.52 |
Symmetry | |
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Space Group | P 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 PILATUS3 6M | 2016-04-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9785 | Diamond | I24 |
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 | 1.86 | 73.72 | 95.8 | 7.8 | 3.4 | 222236 |
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 | apo PCY1 | 1.86 | 73.72 | 222236 | 11725 | 95.75 | 0.19445 | 0.19295 | 0.22338 | RANDOM | 27.171 |
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] | |
-0.58 | 0.79 | 0.63 | 0.27 | -0.75 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.177 |
r_dihedral_angle_4_deg | 17.865 |
r_dihedral_angle_3_deg | 12.381 |
r_long_range_B_other | 6.682 |
r_long_range_B_refined | 6.678 |
r_dihedral_angle_1_deg | 6.333 |
r_scangle_other | 4.988 |
r_scbond_it | 3.337 |
r_scbond_other | 3.337 |
r_mcangle_it | 2.815 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23233 |
Nucleic Acid Atoms | |
Solvent Atoms | 930 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
PHASER | phasing |