2OKR
Crystal Structure of the P38a-MAPKAP kinase 2 Heterodimer
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LEZ | PDB entry 1LEZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 298 | 25% Peg 3350, 250 mM Sodium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.55 | α = 90 |
b = 81.55 | β = 90 |
c = 121.36 | 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 | 95 | CCD | ADSC QUANTUM 210 | 2005-04-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0 | ALS | 5.0.2 |
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 | 40.78 | 98.6 | 0.059 | 9 | 3.06 | 60104 | 1 | 1 | 31.6 |
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) | |||||||||||
2 | 2.07 | 90.7 | 0.364 | 2.2 | 2.48 | 5517 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1LEZ | 2 | 8.48 | 60104 | 2981 | 98.6 | 0.2385 | 0.2385 | 0.2392 | 0.2721 | random | 16.049 |
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] | |
4.8961785 | 4.8961785 | -9.79235699 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
o_angle_torsion | 22.36 |
o_angle_deg | 1.193 |
o_bond_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5792 |
Nucleic Acid Atoms | |
Solvent Atoms | 197 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
d*TREK | data reduction |
autoBUSTER | refinement |