7VDR
The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3O0G |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5.5 | 291 | 0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.83 | α = 90 |
b = 117.83 | β = 90 |
c = 154.93 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | PIXEL | DECTRIS EIGER X 9M | 2019-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.920126 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.55 | 29.65 | 99.9 | 0.145 | 0.149 | 0.033 | 0.999 | 18.4 | 20.8 | 41128 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.55 | 2.65 | 100 | 1.853 | 1.897 | 0.406 | 0.714 | 21.8 |
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 | 3O0G | 2.55 | 29.65 | 39112 | 1980 | 99.91 | 0.2206 | 0.2188 | 0.2558 | RANDOM | 78.045 |
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] | |
0.49 | 0.24 | 0.49 | -1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.975 |
r_dihedral_angle_4_deg | 18.677 |
r_dihedral_angle_3_deg | 16.062 |
r_dihedral_angle_1_deg | 6.306 |
r_angle_refined_deg | 1.32 |
r_angle_other_deg | 1.125 |
r_chiral_restr | 0.056 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6849 |
Nucleic Acid Atoms | |
Solvent Atoms | 69 |
Heterogen Atoms | 112 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |