8CMK
Transportin-3 TNPO3 in complex with RSY region of CIRBP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4C0P |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | 0.5ul Protein (TNPO3) 12mg/ml with 0.2ul Ligand (CIRBP) 4.4mg/ml and 0.1ul seeding stock were mixed with 0.5ul of condition. Condition: 0.1M Sodium HEPES, 0.1M MOPS (acid), 7.5pH, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 0.05% w/v D-Salicin, 0.05% w/v Esculin hydrate, 0.05% w/v Quinine hemisulfate salt monohydrate, 0.05% w/v Tryptamine, 0.05% w/v Arbutin (in 50% EtOH) Protein and Ligand in 50mM Tris, 150mM NaCl, 2mM TCEP, 0.04% NaN3, pH: 7.5 Buffer |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.526 | α = 90 |
b = 101.805 | β = 111.128 |
c = 114.133 | 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 X 16M | 2021-02-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.033220 | PETRA III, DESY | P11 |
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 | 2.94 | 48.72 | 98.5 | 0.094 | 0.13 | 0.09 | 0.996 | 8 | 3.5 | 43555 |
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 | 2.94 | 3.06 | 0.672 | 0.923 | 0.629 | 0.509 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.945 | 48.715 | 43523 | 2105 | 98.273 | 0.25 | 0.2464 | 0.3166 | 83.416 |
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] | |
-0.559 | 1.168 | -1.677 | 1.027 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 16.25 |
r_dihedral_angle_3_deg | 15.385 |
r_lrange_other | 14.689 |
r_lrange_it | 14.688 |
r_mcangle_it | 7.991 |
r_mcangle_other | 7.991 |
r_scangle_it | 7.825 |
r_scangle_other | 7.825 |
r_dihedral_angle_2_deg | 7.16 |
r_dihedral_angle_1_deg | 7.051 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14632 |
Nucleic Acid Atoms | |
Solvent Atoms | 172 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |