2Q9O
Near-atomic resolution structure of a Melanocarpus albomyces laccase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 295 | 15% PMME 2000, 0.2 M ammonium sulphate, 0.1 M sodium acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 173.74 | α = 90 |
b = 61.9 | β = 96.36 |
c = 124.21 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | 0.93100 | ESRF | ID14-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.3 | 20 | 96.7 | 0.078 | 11.4 | 321397 | 310642 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.3 | 1.4 | 91.5 | 0.419 | 3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | AB INITIO | FREE R | 1.3 | 15 | 294994 | 294994 | 15526 | 91.9 | 0.1674 | 0.1674 | 0.1674 | 0.17 | 0.2124 | 0.21 | RANDOM | 13.989 |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
31 | 10679.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.07 |
s_zero_chiral_vol | 0.06 |
s_from_restr_planes | 0.0303 |
s_angle_d | 0.028 |
s_similar_adp_cmpnt | 0.018 |
s_approx_iso_adps | 0.018 |
s_anti_bump_dis_restr | 0.017 |
s_bond_d | 0.01 |
s_rigid_bond_adp_cmpnt | 0.003 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8740 |
Nucleic Acid Atoms | |
Solvent Atoms | 1443 |
Heterogen Atoms | 500 |
Software
Software | |
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Software Name | Purpose |
SHELX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
SHELX | phasing |
SHELXL-97 | refinement |