6RYX
Copper oxidase from Colletotrichum graminicola
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5C86 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 291 | PEG 4000, sodium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 172.043 | α = 90 |
b = 172.043 | β = 90 |
c = 172.043 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | 2018-09-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91587 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 2.65 | 121.65 | 100 | 0.215 | 0.045 | 0.998 | 12 | 24.2 | 24743 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.65 | 2.78 | 100 | 0.581 | 0.535 | 23.3 |
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 | 5C86 | 2.65 | 121.65 | 23451 | 1228 | 99.99 | 0.2241 | 0.221 | 0.2797 | RANDOM | 51.754 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.897 |
r_dihedral_angle_4_deg | 21.761 |
r_dihedral_angle_3_deg | 17.236 |
r_dihedral_angle_1_deg | 8.318 |
r_angle_refined_deg | 1.668 |
r_angle_other_deg | 1.246 |
r_chiral_restr | 0.061 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4567 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
REFMAC | phasing |