5LUR
An avidin mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4U46 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | Drop size: 150 nl of protein-ligand solution and well solution. Protein-ligand solution: 1.8 mg/ml of protein solution (20 mM sodium phosphate, 1M sodium chloride, 20mM imidazole, pH 7.4) and 50 mM ligand solution (1.57 mg in 100 microL of water) were mixed in 10:1 (v/v) ratio. Well solution: 0.18 M sodium chloride, 0.09 M sodium cacodylate (pH 6.5) and 1.8 M ammonium sulfate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.13 | α = 90 |
b = 80.35 | β = 90 |
c = 43.42 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 4M | 2016-02-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9677 | ESRF | MASSIF-3 |
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 | 2.7 | 19.56 | 96.3 | 0.12 | 0.99 | 10.37 | 3.8 | 7458 | -3 |
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 | 2.7 | 2.8 | 98.7 | 0.6 | 0.7 | 2.11 | 4 |
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 | 4U46 | 2.7 | 19.56 | 7073 | 370 | 96.19 | 0.17971 | 0.17662 | 0.23995 | RANDOM | 36.703 |
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] | |
2.05 | 0.56 | -2.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.898 |
r_dihedral_angle_3_deg | 18.244 |
r_dihedral_angle_4_deg | 16.997 |
r_dihedral_angle_1_deg | 7.47 |
r_long_range_B_refined | 6.89 |
r_long_range_B_other | 6.89 |
r_scangle_other | 4.602 |
r_mcangle_it | 3.862 |
r_mcangle_other | 3.862 |
r_scbond_it | 2.751 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1858 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |