5F0P
Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5F0L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 291 | 0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.52 | 65.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 371.29 | α = 90 |
b = 75.32 | β = 97.66 |
c = 57.27 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 PILATUS 6M | 2015-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.97895 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.77 | 56.761 | 99.1 | 0.066 | 0.078 | 0.999 | 12.17 | 77507 | -3 | 80.168 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.77 | 2.94 | 95.3 | 0.904 | 1.073 | 0.808 | 1.33 |
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 | 5F0L | 2.78 | 56.76 | 36032 | 1901 | 95.13 | 0.2209 | 0.2189 | 0.2605 | RANDOM | 70.57 |
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] | |
-0.04 | -0.73 | 0.09 | 0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.632 |
r_dihedral_angle_4_deg | 14.651 |
r_dihedral_angle_3_deg | 13.526 |
r_dihedral_angle_1_deg | 5.79 |
r_mcangle_it | 4.414 |
r_mcbond_it | 2.512 |
r_mcbond_other | 2.512 |
r_angle_refined_deg | 1.135 |
r_angle_other_deg | 0.851 |
r_chiral_restr | 0.064 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7453 |
Nucleic Acid Atoms | |
Solvent Atoms | 42 |
Heterogen Atoms | 135 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |