7NLV
WILDTYPE CORE-STREPTAVIDIN WITH a conjugated BIOTINYLATED PYRROLIDINE II
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6GH7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 25 mg/mL protein in deionised water is mixed at equal volume with 52% MPD. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.32 | α = 90 |
b = 97.6 | β = 110.26 |
c = 50.9 | 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 | PIXEL | DECTRIS EIGER2 XE 16M | 2018-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.915870 | Diamond | I04 |
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 | 1.29 | 46.27 | 99.5 | 0.052 | 0.073 | 0.052 | 0.994 | 7.3 | 1.9 | 112641 |
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 | 1.29 | 1.31 | 0.49 | 0.694 | 0.49 | 0.596 | 1.9 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6GH7 | 1.29 | 46.27 | 112639 | 5708 | 99.405 | 0.209 | 0.2074 | 0.2471 | 23.217 |
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] | |
0.684 | 2.78 | -2.086 | -0.512 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 24.655 |
r_dihedral_angle_4_deg | 15.563 |
r_dihedral_angle_3_deg | 11.277 |
r_rigid_bond_restr | 10.371 |
r_dihedral_angle_1_deg | 8.329 |
r_lrange_it | 4.16 |
r_lrange_other | 3.998 |
r_scangle_it | 3.38 |
r_scangle_other | 3.38 |
r_mcangle_other | 3.107 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3537 |
Nucleic Acid Atoms | |
Solvent Atoms | 280 |
Heterogen Atoms | 84 |
Software
Software | |
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Software Name | Purpose |
Aimless | data reduction |
REFMAC | refinement |
xia2 | data scaling |
MOLREP | phasing |
Coot | model building |