4AZE
Human DYRK1A in complex with Leucettine L41
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VX3 | PDB ENTRY 2VX3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.2 | 0.03 M MGCL2, 22% POLYACRYLIC ACID 5100, 0.1 M HEPES PH 8.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.1 | 69.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.649 | α = 90 |
b = 111.649 | β = 90 |
c = 301.725 | γ = 120 |
Symmetry | |
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Space Group | P 31 1 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 CCD | 2010-02-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 3.15 | 100.57 | 100 | 0.17 | 7.5 | 7.5 | 37756 |
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 | 3.15 | 3.32 | 100 | 0.97 | 1.7 | 6.2 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2VX3 | 3.15 | 100.57 | 35728 | 1883 | 99.72 | 0.21904 | 0.21755 | 0.24831 | RANDOM | 92.693 |
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] | |
2.68 | 1.34 | 2.68 | -4.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.57 |
r_dihedral_angle_4_deg | 18.572 |
r_dihedral_angle_3_deg | 16.327 |
r_dihedral_angle_1_deg | 6.08 |
r_angle_refined_deg | 1.25 |
r_angle_other_deg | 0.889 |
r_chiral_restr | 0.063 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8544 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |