3IW7
Human p38 MAP Kinase in Complex with an Imidazo-pyridine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 100mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.67 | α = 90 |
b = 70.1 | β = 90 |
c = 74.09 | 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 | IMAGE PLATE | MAR scanner 300 mm plate | Osmic | 2009-05-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54170 |
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 | 2.4 | 45 | 98.6 | 0.048 | 25.61 | 3.95 | 14512 | 14316 | -3 | 36.689 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.4 | 2.5 | 97.8 | 0.251 | 6 | 4 | 1627 |
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 1zyj | 2.4 | 37.04 | 14512 | 14315 | 859 | 100 | 0.203 | 0.198 | 0.282 | RANDOM | 30.118 |
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] | |
-0.6 | 0.41 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.289 |
r_dihedral_angle_3_deg | 15.893 |
r_dihedral_angle_4_deg | 14.417 |
r_dihedral_angle_1_deg | 5.839 |
r_scangle_it | 3.095 |
r_scbond_it | 1.969 |
r_mcangle_it | 1.487 |
r_angle_refined_deg | 1.454 |
r_mcbond_it | 0.842 |
r_nbtor_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2705 |
Nucleic Acid Atoms | |
Solvent Atoms | 112 |
Heterogen Atoms | 83 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |
XDS | data reduction |