3WYP
Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2F01 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.2 | 293 | 0.2M ammonium sulfate, 0.1M sodium acetate trihydrate, 24% polyethylene glycol 4000, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.354 | α = 90 |
b = 97.696 | β = 112.29 |
c = 52.57 | 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 | RAYONIX MX225HE | 2011-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.90000 | SPring-8 | BL44XU |
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 | 50 | 96 | 0.046 | 23.4 | 113295 | 110519 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.32 | 93.3 | 0.345 | 2.91 |
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 | 2F01 | 1.3 | 26.69 | 104885 | 5538 | 95.68 | 0.13302 | 0.13061 | 0.17875 | RANDOM | 11.664 |
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] | |
-0.09 | -0.08 | 0.12 | -0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.516 |
r_dihedral_angle_4_deg | 23.126 |
r_dihedral_angle_3_deg | 12.279 |
r_dihedral_angle_1_deg | 7.602 |
r_scangle_it | 6.191 |
r_scbond_it | 4.735 |
r_mcangle_it | 3.668 |
r_rigid_bond_restr | 2.681 |
r_mcbond_it | 2.642 |
r_angle_refined_deg | 2.232 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3630 |
Nucleic Acid Atoms | |
Solvent Atoms | 480 |
Heterogen Atoms | 136 |
Software
Software | |
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Software Name | Purpose |
BSS | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |