3FMJ
P38 kinase crystal structure in complex with 4-(5-Methyl-3-phenyl-isoxazol-4-yl)-pyrimidin-2-ylamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1P38 | PDB entry 1P38 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 290 | 50 mM Hepes pH 7.6, 50 mM CaCl2, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.735 | α = 90 |
b = 85.699 | β = 90 |
c = 126.878 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC QUANTUM 210 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 1.0000 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 50 | 78.7 | 0.098 | 2.9 | 27285 | 26 |
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 | 2.07 | 80.3 | 0.499 | 3.7 | 2.5 | 2723 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 1P38 | 2 | 30.1 | 25843 | 1376 | 78.83 | 0.2167 | 0.21404 | 0.26817 | RANDOM | 27.539 |
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] | |
0.06 | -0.78 | 0.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.301 |
r_dihedral_angle_4_deg | 16.069 |
r_dihedral_angle_3_deg | 12.241 |
r_dihedral_angle_1_deg | 4.67 |
r_scangle_it | 1.705 |
r_scbond_it | 1.043 |
r_angle_refined_deg | 0.994 |
r_mcangle_it | 0.922 |
r_mcbond_it | 0.536 |
r_nbtor_refined | 0.3 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2789 |
Nucleic Acid Atoms | |
Solvent Atoms | 230 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |