4JC8
Crystal Structure of HOPS component Vps33 from Chaetomium thermophilum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 298 | 12% (w/v) PEG 3350, 10 mM barium chloride, pH 8.5, vapor diffusion, sitting drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.936 | α = 90 |
b = 64.436 | β = 91.77 |
c = 151.685 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2012-08-07 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.97930, 0.9640 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.6 | 50 | 99.8 | 0.09 | 15.1 | 3.7 | 43028 | 43028 | -3 | 46.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.74 | 99.9 | 0.09 | 2.6 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | MAD | 2.6 | 35.951 | 1.39 | 43008 | 43008 | 2153 | 99.73 | 0.1877 | 0.1846 | 0.2469 | Random | 25.2416 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.788 |
f_angle_d | 1.218 |
f_chiral_restr | 0.076 |
f_bond_d | 0.009 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9340 |
Nucleic Acid Atoms | |
Solvent Atoms | 225 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SHARP | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |