5L2W
The X-ray co-crystal structure of human CDK2/CyclinE and Dinaciclib.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1W98 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 286.15 | PEG20K, 180mM Mg(HCO2)2, 0.1M MES pH 6.0 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.73 | 55.03 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 100.307 | α = 90 |
| b = 100.307 | β = 90 |
| c = 151.857 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 98.15 | PIXEL | DECTRIS PILATUS3 S 6M | 2015-11-09 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.8 | 45 | 99.9 | 22.9 | 12.76 | 19770 | 100.25 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | FOURIER SYNTHESIS | THROUGHOUT | 1W98 | 2.8 | 45 | 19741 | 962 | 99.99 | 0.2019 | 0.1995 | 0.2463 | RANDOM | 84.34 | ||||||
| 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] | |
| -6.1078 | -6.1078 | 12.2156 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| t_other_torsion | 21.34 |
| t_omega_torsion | 2.72 |
| t_angle_deg | 1.15 |
| t_bond_d | 0.01 |
| t_dihedral_angle_d | |
| t_incorr_chiral_ct | |
| t_pseud_angle | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4608 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 75 |
| Heterogen Atoms | 35 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| BUSTER | refinement |
| autoXDS | data processing |
| BUSTER | phasing |
| Aimless | data scaling |
