2PMI
Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal Transduction Pathway with Bound ATP-gamma-S
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PK9 | PDB ENTRY 2PK9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 283 | 9ul 12% PEG 10000, 10% glycerol, 0.05 M strontium chloride (SrCl2), 10 mM Tris (2-carboxyethyl) phosphine (TCEP, 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.74 | 74.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 146.592 | α = 90 |
b = 146.592 | β = 90 |
c = 212.848 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 200 | CCD | ADSC QUANTUM 4 | APS 19ID | 2006-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.0332 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.9 | 14.98 | 91.1 | 0.099 | 0.099 | 11 | 3.1 | 53704 | 53704 | 1 | 33.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.9 | 3 | 75.6 | 0.248 | 0.248 | 2.4 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2PK9 | 2.9 | 14.98 | 53704 | 53533 | 2707 | 91.2 | 0.289 | 0.289 | 0.325 | RANDOM | 49.5 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.43 | 0.43 | -0.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22 |
c_scangle_it | 7.76 |
c_mcangle_it | 6.07 |
c_scbond_it | 5.27 |
c_mcbond_it | 3.77 |
c_improper_angle_d | 1.94 |
c_angle_deg | 1.3 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8083 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |