4MAI
Structure of Aspergillus oryzae AA11 Lytic Polysaccharide Monooxygenase with Cu(I)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6 | 292 | 10 mM zinc chloride, 100 mM MES, pH 6.0, 20% w/v PEG6000, crystals soaked in solution containing 2 mM copper chloride to replace zinc, VAPOR DIFFUSION, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 48.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.269 | α = 90 |
b = 60.629 | β = 90 |
c = 65.176 | 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 | 2013-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.980 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (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 | 1.4 | 44.39 | 99.3 | 0.052 | 0.033 | 17.9 | 6.3 | 44262 | 44262 | 1 | 1 | 11.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.4 | 1.42 | 95.7 | 0.742 | 2 | 5.1 | 2093 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | ISOTROPIC STRUCTURE REFINEMENT | THROUGHOUT | 1.4 | 42.63 | 44262 | 42001 | 2200 | 99.07 | 0.1323 | 0.1323 | 0.1314 | 0.1507 | RANDOM | 18.6373 |
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] | |
-0.4 | 0.13 | 0.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 33.16 |
r_dihedral_angle_2_deg | 30.329 |
r_dihedral_angle_4_deg | 22.076 |
r_sphericity_bonded | 10.715 |
r_dihedral_angle_3_deg | 8.866 |
r_dihedral_angle_1_deg | 7.003 |
r_mcangle_it | 2.352 |
r_rigid_bond_restr | 2.204 |
r_mcbond_it | 1.81 |
r_mcbond_other | 1.81 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1377 |
Nucleic Acid Atoms | |
Solvent Atoms | 187 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
SHELX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |