5W2I
Crystal structure of the core catalytic domain of human inositol phosphate multikinase soaked with C4-analogue of PtdIns(4,5)P2 and ADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 298 | 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structures, the apo crystal were further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 20 mM C4-analogue of PtdIns(4,5)P2, 10 mM Mg and 5mM ATP for 1 day. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 44.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.09 | α = 90 |
b = 78.09 | β = 90 |
c = 86.32 | γ = 90 |
Symmetry | |
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Space Group | P 42 21 2 |
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 | RAYONIX MX300-HS | 2016-08-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1 | APS | 22-ID |
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 | 1.6 | 50 | 99.9 | 0.097 | 22.1 | 7.7 | 36175 |
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 | 1.6 | 1.63 | 100 | 0.727 | 2.9 | 7.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.6 | 34.03 | 34007 | 1813 | 98.91 | 0.17148 | 0.16922 | 0.21525 | RANDOM | 19.146 |
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] | |
-0.07 | -0.07 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 34.306 |
r_dihedral_angle_2_deg | 31.484 |
r_sphericity_bonded | 13.196 |
r_dihedral_angle_4_deg | 13.098 |
r_dihedral_angle_3_deg | 12.87 |
r_dihedral_angle_1_deg | 5.759 |
r_long_range_B_refined | 4.861 |
r_long_range_B_other | 3.944 |
r_scangle_other | 2.126 |
r_scbond_it | 1.807 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1943 |
Nucleic Acid Atoms | |
Solvent Atoms | 182 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |