3WGW
Structure of PCNA bound to a small molecule inhibitor
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3VKX | |
Crystallization
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.13 | 76.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 192.173 | α = 90 |
| b = 192.173 | β = 90 |
| c = 192.173 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 3 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | CCD | ADSC QUANTUM 270 | 2012-03-03 | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1 | Photon Factory | AR-NE3A |
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 | 20 | 30376 | ||||||||||||||||
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 (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3VKX | 2.8 | 20 | 28719 | 1532 | 99.38 | 0.18381 | 0.18181 | 0.18 | 0.22125 | 0.22 | RANDOM | 42.32 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 47.095 |
| r_dihedral_angle_4_deg | 21.236 |
| r_dihedral_angle_3_deg | 20.889 |
| r_dihedral_angle_1_deg | 8.238 |
| r_angle_refined_deg | 2.419 |
| r_chiral_restr | 0.154 |
| r_bond_refined_d | 0.02 |
| r_gen_planes_refined | 0.009 |
| r_bond_other_d | |
| r_angle_other_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3820 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 126 |
| Heterogen Atoms | 73 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
