5V8G
Pekin duck lysozyme isoform I (DEL-I)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IEE | PDB entry 1IEE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 200 mM potassium thiocyanate, 100 mM Bis-Tris-propane, pH 8.5, 20% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.89 | 35.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 28.2 | α = 90 |
b = 65.4 | β = 113.24 |
c = 31.64 | 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 | ADSC QUANTUM 315r | 2016-06-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
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 | 1.2 | 32.7 | 93.5 | 0.08 | 0.09 | 0.041 | 0.996 | 10.2 | 4.7 | 30531 | 9.9 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.2 | 1.22 | 88.6 | 0.481 | 0.547 | 0.255 | 0.847 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
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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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1IEE | 1.2 | 32.7 | 28891 | 1613 | 93 | 0.1468 | 0.145 | 0.1803 | RANDOM | 15.336 |
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] | |
0.25 | 0.16 | 0.9 | -0.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.591 |
r_sphericity_free | 35.426 |
r_dihedral_angle_4_deg | 14.311 |
r_dihedral_angle_3_deg | 11.119 |
r_sphericity_bonded | 9.541 |
r_dihedral_angle_1_deg | 6.096 |
r_rigid_bond_restr | 1.885 |
r_angle_refined_deg | 1.578 |
r_angle_other_deg | 1.071 |
r_chiral_restr | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 966 |
Nucleic Acid Atoms | |
Solvent Atoms | 115 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data collection |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |