6RI8
Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by fluoride anions at sub-atomic resolution. Third structure of the series with 800 KGy dose.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5E9N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4 | 294 | CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (12MG/ML, 20 MM K-PHOSPHATE BUFFER, PH 6.5) RESERVOIR SOLUTION (0.1 M CITRATE-PHOSPHATE BUFFER PH 4.0, 0.2 M AMMONIUM ACETATE, 25% PEG 4000). Before collecting the diffraction data, the crystal was soaked in reservoir solution containing 0.1 M NaF. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.18 | α = 90 |
b = 84.2 | β = 90 |
c = 112.22 | 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 | 2017-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.886 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | 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 | 0.95 | 70 | 97.2 | 0.077 | 0.996 | 11.6 | 4.4 | 323608 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 0.95 | 0.97 | 82.3 | 0.698 | 0.716 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 5E9N | 0.95 | 67.35 | 307589 | 16019 | 97.17 | 0.10616 | 0.10552 | 0.11854 | RANDOM | 12.604 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.35 | -0.38 | 0.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.949 |
r_dihedral_angle_4_deg | 22.595 |
r_sphericity_free | 18.027 |
r_dihedral_angle_3_deg | 10.958 |
r_sphericity_bonded | 8.825 |
r_dihedral_angle_1_deg | 7.152 |
r_rigid_bond_restr | 4.094 |
r_long_range_B_refined | 2.697 |
r_long_range_B_other | 2.197 |
r_scangle_other | 2.024 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3765 |
Nucleic Acid Atoms | |
Solvent Atoms | 974 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |