1TZL
Crystal Structure of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | PEG 6000, MES, tributyl phosphine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 164.879 | α = 90 |
b = 103.596 | β = 105.25 |
c = 169.169 | 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 | CCD | MARRESEARCH | N2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror | 2003-06-14 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.97934, 0.97950, 0.93926 | SLS | X06SA |
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 | 2.35 | 20 | 96.1 | 0.092 | 0.066 | 8.42 | 2 | 228044 | 228044 | 3.99 | 3.99 | 33.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.35 | 2.42 | 94.9 | 0.295 | 0.21 | 3.99 | 2 | 35967 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | MAD | THROUGHOUT | 2.35 | 19.7 | 3.99 | 3.99 | 228316 | 219141 | 9088 | 99.96 | 0.17604 | 0.17604 | 0.17398 | 0.22575 | RANDOM | 20.96 |
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] | |
-0.77 | -1.04 | -1.85 | 2.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.809 |
r_scangle_it | 3.903 |
r_scbond_it | 2.572 |
r_angle_refined_deg | 1.45 |
r_mcangle_it | 1.436 |
r_mcbond_it | 0.764 |
r_symmetry_hbond_refined | 0.234 |
r_nbd_refined | 0.207 |
r_symmetry_vdw_refined | 0.172 |
r_xyhbond_nbd_refined | 0.152 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 36392 |
Nucleic Acid Atoms | |
Solvent Atoms | 2154 |
Heterogen Atoms | 424 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
XDS | data scaling |
MLPHARE | phasing |