6FL2
Crystal structure of a dye-decolorizing peroxidase D143A variant from Klebsiella pneumoniae (KpDyP)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298.15 | 23% w/v PEG 3350, 0.1 M MgCl2, 0.1 M Tris-HCl, pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.76 | α = 90 |
b = 76.69 | β = 107.79 |
c = 76.14 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS3 2M | 2017-06-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.27 | 52.69 | 97.21 | 0.03012 | 0.03792 | 0.02269 | 0.999 | 16.61 | 1.4 | 346778 | 142004 | 12.7807580788 |
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 | 1.27 | 1.315 | 96.98 | 0.4241 | 0.5324 | 0.3181 | 0.794 | 2.63 | 2.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6FKS | 1.27000110594 | 52.6839422655 | 1.34751905903 | 141989 | 6954 | 97.2141204179 | 0.115502274903 | 0.114210014854 | 0.140849286858 | 18.6598735573 |
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 |
f_dihedral_angle_d | 14.941459685 |
f_angle_d | 1.07538563247 |
f_chiral_restr | 0.0826241502766 |
f_bond_d | 0.00950616898532 |
f_plane_restr | 0.00747746439931 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4677 |
Nucleic Acid Atoms | |
Solvent Atoms | 795 |
Heterogen Atoms | 106 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |