2C6L
Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1B39 | PDB ENTRY 1B39 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | PEG3350, HEPES PH7.2, AMMONIUM ACETATE, VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, pH 7.20 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 39.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 53.664 | α = 90 |
| b = 71.806 | β = 90 |
| c = 72.083 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU MSC | MIRRORS | 2003-05-01 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RUH3R | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.9 | 30 | 92.2 | 0.09 | 5.9 | 4.75 | 20904 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.9 | 1.96 | 81.1 | 0.4 | 1.8 | 3.72 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1B39 | 2.3 | 15 | 10800 | 974 | 91.8 | 0.185 | 0.176 | 0.281 | RANDOM | 42.08 | ||||||
| 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] | |
| 0.84 | -1.8 | 0.97 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 5.772 |
| r_angle_refined_deg | 1.389 |
| r_chiral_restr | 0.257 |
| r_nbd_refined | 0.211 |
| r_symmetry_vdw_refined | 0.2 |
| r_xyhbond_nbd_refined | 0.191 |
| r_symmetry_hbond_refined | 0.174 |
| r_bond_refined_d | 0.013 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2340 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 241 |
| Heterogen Atoms | 28 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystalClear | data reduction |
| d*TREK | data scaling |
| MOLREP | phasing |
