6HD0
Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 6% (v/v) PEG1500, 0.2M sodium acetate, 0.1M Hepes pH 7.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.5 | 64.83 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 185.12 | α = 90 |
b = 185.12 | β = 90 |
c = 122.426 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2014-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.728 | 48.98 | 90.7 | 0.306 | 0.34 | 0.148 | 0.983 | 6.2 | 5.3 | 28980 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.88 | 4.03 | 98.1 | 0.2686 | 0.324 | 0.75 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1S3S, 5IFS | 3.728 | 48.98 | 26254 | 2606 | 58.94 | 0.2117 | 0.2077 | 0.2529 | RANDOM | 123.914 |
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] | |
-50.75 | -50.75 | 101.5 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 24.589 |
r_dihedral_angle_4_deg | 11.934 |
r_dihedral_angle_3_deg | 11.257 |
r_dihedral_angle_1_deg | 4.187 |
r_angle_refined_deg | 1.168 |
r_angle_other_deg | 1.04 |
r_chiral_restr | 0.033 |
r_gen_planes_refined | 0.003 |
r_bond_refined_d | 0.002 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 24272 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 162 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |