6PU0
Pigeon Cryptochrome4 bound to flavin adenine dinucleotide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4K0R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 294.15 | Crystals were obtained at 21C in dark from a 1:1 mixture of protein (10-12 mg/mL) and a reservoir solution consisting of 5% PEG 6000 and 0.1 M HEPES pH 7.1. Crystal reached maximum size after 4-5 days and were harvested at that time in the dark. Crystals were transferred to cryoprotectant solution consisting of 5% PEG 6000, 0.1 M HEPES pH 7, 2 mM DTT and either 30% P400 or 30% glycerol. Crystals were flash-frozen in liquid nitrogen in the dark |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.099 | α = 90 |
b = 86.578 | β = 90 |
c = 104.267 | 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 | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2017-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.979200 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.849 | 104.073 | 94.2 | 0.097 | 0.994 | 13.5 | 3.4 | 41952 | 16.1759252839 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.9 | 1.97 | 0.438 | 0.816 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 4K0R | 1.8979 | 48.0201133545 | 1.36385614405 | 37182 | 2000 | 94.1578667477 | 0.159897807 | 0.157855371182 | 0.195095045293 | 19.0193492644 |
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 | 19.7419480971 |
f_angle_d | 0.859910339667 |
f_chiral_restr | 0.0537102738096 |
f_bond_d | 0.00686993068116 |
f_plane_restr | 0.00593814286363 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3938 |
Nucleic Acid Atoms | |
Solvent Atoms | 321 |
Heterogen Atoms | 101 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |