6RI0
Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by chloride anions at sub-atomic resolution. Ninth structure of the series with 1215 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 NaCl. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.15 | α = 90 |
b = 84.06 | β = 90 |
c = 112.04 | 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 | 1 | 70 | 99.6 | 0.075 | 0.995 | 10 | 4.6 | 283692 |
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 | 1 | 1.03 | 99.9 | 0.853 | 0.741 | 2 |
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 | 5E9N | 1 | 67.24 | 269675 | 14017 | 99.61 | 0.12066 | 0.11984 | 0.13677 | RANDOM | 10.881 |
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] | |
-0.05 | 0.03 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.955 |
r_sphericity_free | 22.18 |
r_dihedral_angle_4_deg | 21.724 |
r_sphericity_bonded | 12.481 |
r_dihedral_angle_3_deg | 10.654 |
r_dihedral_angle_1_deg | 7.089 |
r_rigid_bond_restr | 4.979 |
r_long_range_B_refined | 2.884 |
r_long_range_B_other | 2.279 |
r_scangle_other | 2.176 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3765 |
Nucleic Acid Atoms | |
Solvent Atoms | 796 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |