3OJK
Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase in complex with 4-nitrocatechol at 1.68 Ang resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2IG9 | PDB entry 2IG9 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 13% PEG6000, 0.1 M calcium chloride, 0.1 M Tris-HCl. Cryoprotectant 25% PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.38 | 48.27 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 110.102 | ¦Á = 90 |
| b = 150.395 | ¦Â = 90 |
| c = 95.941 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | 100 | CCD | ADSC QUANTUM 315r | 2010-03-21 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.9801 | SOLEIL | PROXIMA 1 |
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 | 1.68 | 41.19 | 97.2 | 0.053 | 10.6 | 5.8 | 180226 | 175180 | 3 | 18.8 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1.68 | 1.77 | 91.7 | 0.346 | 0.742 | 2.1 | 4.8 | 23848 | ||||||||||||
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 2IG9 | 1.68 | 37.96 | 166376 | 8696 | 96.67 | 0.15443 | 0.153 | 0.18153 | RANDOM | 20.873 | ||||||
| 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] | |
| -0.03 | 0.02 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.183 |
| r_dihedral_angle_4_deg | 18.926 |
| r_dihedral_angle_3_deg | 12.729 |
| r_dihedral_angle_1_deg | 7.023 |
| r_scangle_it | 3.113 |
| r_scbond_it | 2.015 |
| r_angle_refined_deg | 1.46 |
| r_mcangle_it | 1.147 |
| r_angle_other_deg | 0.911 |
| r_mcbond_it | 0.696 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11512 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1369 |
| Heterogen Atoms | 176 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOLREP | phasing |
| REFMAC | refinement |
| MxCuBE | data collection |
| XDS | data reduction |
| SCALA | data scaling |
