6XIZ
Crystal structure of multi-copper oxidase from Pediococcus acidilactici
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 292 | 52.5 nL drop composed of 95 mM Sodium Citrate buffer, pH 3.0, 3% polyethylene glycol 8000, 7.8% polyethylene glycol 400, 1.2% dimethyl sulfoxide, 114 mM benzamidine hydrochloride, and 5.0-10.0 mg/mL protein in 5 mM Tris-HCL pH 7.2 Mylar was initially used as the surface, resulting in thin polycrystalline needles. Changing the surface to COC (cyclic olefin copolymer) resulted in large high-quality single crystals. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.06 | α = 90 |
b = 147.3 | β = 98.55 |
c = 65.46 | 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 EIGER X 9M | 2019-08-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.9202 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.78 | 73.65 | 98.3 | 0.185 | 0.999 | 10.37 | 25.53 | 98773 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.78 | 1.82 | 77.6 | 0.4263 | 0.476 | 0.71 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.8 | 73.65 | 92098 | 4742 | 99.97 | 0.11624 | 0.1139 | 0.161 | RANDOM | 47.028 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.44 | 1 | -0.23 | -0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.007 |
r_sphericity_free | 29.463 |
r_sphericity_bonded | 18.229 |
r_dihedral_angle_3_deg | 18.097 |
r_dihedral_angle_4_deg | 17.055 |
r_scangle_other | 9.509 |
r_scbond_it | 9.229 |
r_scbond_other | 9.229 |
r_long_range_B_refined | 8.301 |
r_long_range_B_other | 8.226 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7622 |
Nucleic Acid Atoms | |
Solvent Atoms | 609 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |