2Z5B
Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 25mM MES, 50mM KH2PO4, 16%(w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
2 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 0.1M HEPES, 4.1M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.487 | α = 90 |
b = 57.487 | β = 90 |
c = 82.206 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 | CCD | Bruker DIP-6040 | 2006-07-18 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | Bruker DIP-6040 | 2006-12-09 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9000 | SPring-8 | BL44XU |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.96408, 0.97925, 0.97945 | SPring-8 | BL44XU |
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 | 1.96 | 49.81 | 98 | 0.059 | 24.6 | 4 | 21419 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1.96 | 2.03 | 93.7 | 0.187 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.96 | 49.81 | 20240 | 1096 | 97.9 | 0.24185 | 0.23953 | 0.24 | 0.28727 | 0.28 | RANDOM | 40.874 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
1.37 | 0.69 | 1.37 | -2.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.382 |
r_dihedral_angle_4_deg | 20.243 |
r_dihedral_angle_3_deg | 17.504 |
r_dihedral_angle_1_deg | 7.558 |
r_scangle_it | 2.558 |
r_scbond_it | 1.722 |
r_mcangle_it | 1.72 |
r_angle_refined_deg | 1.393 |
r_mcbond_it | 1.014 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2077 |
Nucleic Acid Atoms | |
Solvent Atoms | 31 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |