1P4F
DEATH ASSOCIATED PROTEIN KINASE CATALYTIC DOMAIN WITH BOUND INHIBITOR FRAGMENT
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JKL | PDB entry 1JKL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 297 | Ammonium sulfate, Tris, MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.89 | 34.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.238 | α = 90 |
b = 62.527 | β = 90 |
c = 88.927 | 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 | MARRESEARCH | 2002-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 1.0 | APS | 5ID-B |
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 | 1.9 | 30 | 97.9 | 0.049 | 25.8 | 4 | 20869 | 20869 | -3 | -3 |
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) | |||||||||||
1.9 | 1.97 | 97.3 | 0.213 | 5.52 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 1JKL | 1.9 | 20 | 20190 | 19405 | 778 | 94.88 | 0.18641 | 0.18454 | 0.2328 | RANDOM | 21.135 |
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] | |
0.37 | 0.69 | -1.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.375 |
r_dihedral_angle_4_deg | 20.125 |
r_dihedral_angle_3_deg | 13.251 |
r_dihedral_angle_1_deg | 5.137 |
r_scangle_it | 3.195 |
r_scbond_it | 2.064 |
r_mcangle_it | 1.31 |
r_angle_refined_deg | 1.216 |
r_mcbond_it | 0.993 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2210 |
Nucleic Acid Atoms | |
Solvent Atoms | 182 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
CNS | refinement |
CNS | phasing |
MAR345 | data collection |