5NKZ
Crystal structure of H. polymorpha ubiquitin conjugating enzyme Pex4p in complex with soluble domain of Pex22p
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Y9M | Pex4:Pex22 complex coordinates from S. cerevisae (PDB: 2Y9M(Williams et al. 2012); 33/57 % and 14/35 % identity/similarity, respectively) as starting model |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.1 M BIS-TRIS Propane pH 7.8, 0.2 M sodium sulphate, 22 % w/v PEG-3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.82 | 56.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.683 | α = 89.18 |
b = 61.582 | β = 78.02 |
c = 78.441 | γ = 84.09 |
Symmetry | |
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Space Group | P 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 PILATUS3 6M | 2016-07-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 0.98 | PETRA III, DESY | P11 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.85 | 48.0397 | 95.02 | 0.123 | 6.03 | 3.93 | 20450 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.85 | 2.95 | 94.5 | 0.8 | 1.14 | 5.49 |
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 | Pex4:Pex22 complex coordinates from S. cerevisae (PDB: 2Y9M(Williams et al. 2012); 33/57 % and 14/35 % identity/similarity, respectively) as starting model | 2.85 | 48.0397 | 18451 | 980 | 95.02 | 0.2385 | 0.23608 | 0.2837 | RANDOM | 74.337 |
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] | |
2.85 | -0.04 | -2.49 | -0.81 | 5.69 | -3.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.019 |
r_dihedral_angle_4_deg | 23.592 |
r_dihedral_angle_3_deg | 20.173 |
r_dihedral_angle_1_deg | 8.281 |
r_long_range_B_refined | 6.058 |
r_long_range_B_other | 6.058 |
r_mcangle_it | 3.826 |
r_mcangle_other | 3.825 |
r_scangle_other | 3.657 |
r_mcbond_it | 2.327 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4639 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
MOLREP | phasing |
Aimless | data scaling |