4IXP
Crystal structure of Maternal Embryonic Leucine Zipper Kinase (MELK)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FE3 | PDB ENTRY 3FE3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 294 | 0.1 M Sodium Cacodylate, 0.7M Sodium Acetate, 2% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.03 | 75.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 135.449 | α = 90 |
b = 135.449 | β = 90 |
c = 153.652 | γ = 120 |
Symmetry | |
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Space Group | P 64 2 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 | ADSC QUANTUM 315r | 2011-05-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.97915 | SSRF | BL17U |
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 | 2.749 | 50 | 99.8 | 0.059 | 30 | 7 | 22247 | 22247 | 2 | 2 | 60.54 |
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 | 2.749 | 2.8 | 100 | 0.473 | 4.6 | 7.3 | 1076 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | PDB ENTRY 3FE3 | 2.749 | 34.847 | 1.34 | 22206 | 22206 | 1134 | 99.87 | 0.2019 | 0.2035 | 0.2019 | 0.2323 | RANDOM |
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] | |
7.9904 | 7.9904 | -15.9808 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.843 |
f_angle_d | 1.11 |
f_chiral_restr | 0.072 |
f_bond_d | 0.008 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2719 |
Nucleic Acid Atoms | |
Solvent Atoms | 39 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |