7ZN6
Crystal structure of laccase-like multicopper oxidase (LMCO) from Thermothelomyces thermophilus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M NH4Cl 18% w/v PEG 6000 0.1 M MES pH 5.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.29 | 46.25 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 74.855 | α = 90 |
b = 74.855 | β = 90 |
c = 118.948 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER R 4M | 2021-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9763 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.9 | 118.95 | 100 | 0.105 | 0.114 | 0.043 | 0.999 | 14.8 | 12.9 | 51534 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 1.94 | 1.028 | 1.126 | 0.456 | 0.886 | 11.9 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Alphafold 2.0 | 1.9 | 74.967 | 51486 | 2567 | 99.996 | 0.153 | 0.1516 | 0.1847 | 35.061 |
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] | |
-1.867 | -1.867 | 3.733 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.459 |
r_dihedral_angle_4_deg | 22.054 |
r_dihedral_angle_3_deg | 13.715 |
r_dihedral_angle_1_deg | 8.025 |
r_lrange_it | 5.532 |
r_lrange_other | 5.481 |
r_scangle_it | 2.98 |
r_scangle_other | 2.98 |
r_mcangle_it | 2.282 |
r_mcangle_other | 2.282 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4523 |
Nucleic Acid Atoms | |
Solvent Atoms | 345 |
Heterogen Atoms | 80 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
PDB_EXTRACT | data extraction |
PHASER | phasing |