5VAS
Pekin duck egg lysozyme isoform III (DEL-III), orthorhombic form
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 | 2.4 M ammonium phosphate monobasic, 100 mM Tris, pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.005 | α = 90 |
b = 58.35 | β = 90 |
c = 107.48 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2017-03-11 | 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 | 1.4 | 27.78 | 100 | 0.091 | 0.094 | 0.024 | 0.999 | 17.8 | 14.5 | 55408 |
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 | 1.4 | 1.42 | 100 | 0.912 | 0.946 | 0.249 | 0.848 | 14.1 |
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 | 1.4 | 27.78 | 52574 | 2763 | 99.95 | 0.1451 | 0.1438 | 0.1693 | RANDOM | 15.243 |
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] | |
-0.71 | -0.23 | 0.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.444 |
r_sphericity_free | 27.588 |
r_dihedral_angle_4_deg | 15.377 |
r_dihedral_angle_3_deg | 10.867 |
r_dihedral_angle_1_deg | 6.261 |
r_sphericity_bonded | 4.87 |
r_angle_refined_deg | 1.4 |
r_angle_other_deg | 1.022 |
r_rigid_bond_restr | 0.902 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2012 |
Nucleic Acid Atoms | |
Solvent Atoms | 271 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data collection |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
REFMAC | refinement |