- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full (PDF - gz)
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 2 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
- Biological Assembly 2 (PDB - gz)
2CCH | pdb_00002cch
The crystal structure of CDK2 cyclin A in complex with a substrate peptide derived from CDC modified with a gamma-linked ATP analogue
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1QMZ | PDB ENTRY 1QMZ |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 277 | 13% PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE, 0.1 M CITRATE/ACETATE BUFFER PH 5.6 AT 4 C |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.9 | 57.7 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 74.535 | α = 90 |
| b = 114.483 | β = 90 |
| c = 181.299 | 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 | CCD | ADSC CCD | 2005-11-12 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
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 | 1.7 | 96 | 98 | 0.06 | 15.1 | 3.6 | 167702 | 2 | |||||||||||
| 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 | 1.7 | 1.79 | 91.5 | 0.37 | 2.8 | ||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1QMZ | 1.7 | 96.67 | 159215 | 8410 | 98.2 | 0.15 | 0.148 | 0.2048 | 0.182 | RANDOM | 20.79 | |||||
| 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] | |
| 0.32 | -1.23 | 0.92 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.078 |
| r_dihedral_angle_4_deg | 17.764 |
| r_dihedral_angle_3_deg | 13.909 |
| r_dihedral_angle_1_deg | 5.701 |
| r_scangle_it | 3.895 |
| r_scbond_it | 2.957 |
| r_mcangle_it | 1.983 |
| r_mcbond_it | 1.674 |
| r_angle_refined_deg | 1.59 |
| r_angle_other_deg | 0.894 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.078 |
| r_dihedral_angle_4_deg | 17.764 |
| r_dihedral_angle_3_deg | 13.909 |
| r_dihedral_angle_1_deg | 5.701 |
| r_scangle_it | 3.895 |
| r_scbond_it | 2.957 |
| r_mcangle_it | 1.983 |
| r_mcbond_it | 1.674 |
| r_angle_refined_deg | 1.59 |
| r_angle_other_deg | 0.894 |
| r_symmetry_hbond_refined | 0.364 |
| r_symmetry_vdw_refined | 0.356 |
| r_symmetry_vdw_other | 0.345 |
| r_nbd_refined | 0.233 |
| r_xyhbond_nbd_refined | 0.199 |
| r_nbd_other | 0.194 |
| r_nbtor_refined | 0.18 |
| r_chiral_restr | 0.149 |
| r_nbtor_other | 0.086 |
| r_bond_refined_d | 0.017 |
| r_gen_planes_refined | 0.007 |
| r_gen_planes_other | 0.002 |
| r_bond_other_d | 0.001 |
| r_xyhbond_nbd_other | |
| r_metal_ion_refined | |
| r_metal_ion_other | |
| r_symmetry_hbond_other | |
| r_symmetry_metal_ion_refined | |
| r_symmetry_metal_ion_other | |
| r_mcbond_other | |
| r_mcangle_other | |
| r_scbond_other | |
| r_scangle_other | |
| r_long_range_B_refined | |
| r_long_range_B_other | |
| r_rigid_bond_restr | |
| r_sphericity_free | |
| r_sphericity_bonded | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9148 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1045 |
| Heterogen Atoms | 79 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
