5D9C
Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 7.5 | 293 | mixing purified LRE solution (27 mg/mL LRE, 10 mM HEPES pH 7.5, 0.1 M NaCl, 10% glycerol) and precipitant solution (35% PEG3350, 10% MPD, 0.1 M HEPES pH 7.5, 0.2 M MgCl2) at ratios between 1:2 and 1:1.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.1 | α = 90 |
b = 77.5 | β = 90 |
c = 84.8 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 293 | CCD | MPCCD | 2014-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SACLA BEAMLINE BL3 | 0.984 | SACLA | BL3 |
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 | 25 | 100 | 1.82 | 106.2 | 80855 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SIRAS | FREE R-VALUE | 1.6 | 24.712 | 1.33 | 74044 | 2946 | 91.66 | 0.2034 | 0.2021 | 0.2354 | 28.3727 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.011 |
f_angle_d | 1.452 |
f_chiral_restr | 0.068 |
f_bond_d | 0.014 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2385 |
Nucleic Acid Atoms | |
Solvent Atoms | 164 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SHELXDE | phasing |
CrystFEL | data reduction |