5O3X
Structural characterization of the fast and promiscuous macrocyclase from plant - apo PCY1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QFS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 12.2 mg/mL PCY1 in 33% (w/v) PEG 2000, 113.75 mM Mg formate and 0.1 M Na cacodylate pH 7.0. For cryo protection 10% (v/v) glycerol were added to reservoir solution. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 275.58 | α = 90 |
b = 60.85 | β = 92.65 |
c = 88.04 | 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 | 2015-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 2.55 | 87.95 | 98.3 | 11.5 | 3.3 | 44824 |
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 | 1QFS | 2.55 | 87.95 | 44824 | 2362 | 98.24 | 0.21882 | 0.2165 | 0.26303 | RANDOM | 62.094 |
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] | |
-3.98 | -0.88 | 2.07 | 1.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.877 |
r_dihedral_angle_3_deg | 14.835 |
r_dihedral_angle_4_deg | 14.818 |
r_dihedral_angle_1_deg | 6.444 |
r_long_range_B_refined | 4.152 |
r_long_range_B_other | 4.148 |
r_mcangle_it | 1.395 |
r_mcangle_other | 1.395 |
r_angle_refined_deg | 1.242 |
r_scangle_other | 1.166 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11414 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
PHASER | phasing |