8U8S
Y229F/S292F Streptomyces coelicolor Laccase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CG8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 296 | Crystals were prepared using hanging drop vapor-diffusion technique at room temperature (~296 K). Protein is at a concentration of 18.5 mg/ml in 50 mM H3BO3, 0.1 M NaCl, pH 9.0 buffer. The well buffer contains 0.1 M glycine, 0.3-0.6 M NaCl, pH 9.0, and 37-39% (v/v) PEG (polyethylene glycol) monomethyl ether 550. 500 uL of well buffer is added to each well and protein is mixed with well buffer at a 1.5 uL:1.5 uL ratio. The crystal growth time was ca. 1-2 weeks |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 176.351 | α = 90 |
b = 176.351 | β = 90 |
c = 176.21 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 2M | 2023-06-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97741 | ALS | 5.0.1 |
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 | 2.63 | 78.87 | 99.98 | 0.1839 | 0.996 | 12.37 | 13.3 | 82693 | 46.73 |
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 | 2.63 | 2.724 | 1.204 | 0.744 |
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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.63 | 78.87 | 1.36 | 82685 | 7979 | 99.99 | 0.1694 | 0.1679 | 0.1988 | 45.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.1729 |
f_angle_d | 0.903 |
f_chiral_restr | 0.0553 |
f_plane_restr | 0.0077 |
f_bond_d | 0.0069 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6454 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 223 |
Software
Software | |
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Software Name | Purpose |
BOS | data collection |
xia2 | data scaling |
PHENIX | phasing |
PHENIX | refinement |
xia2 | data reduction |