2GJ4
Structure of rabbit muscle glycogen phosphorylase in complex with ligand
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.7 | 289 | 1.1mM IMP, 1.1mM Spermine, 0mM BES, 2.9mM DTT, 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.51 | 50.93 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 128.128 | ¦Á = 90 |
| b = 128.128 | ¦Â = 90 |
| c = 116.346 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 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 4 | Rh coated Si mirror | 2001-10-24 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SRS BEAMLINE PX9.6 | 0.87 | SRS | PX9.6 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.6 | 48.8 | 74.5 | 0.059 | 0.045 | 12 | 3.3 | 98023 | 94754 | 1 | |||||||||
| 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 | 1.6 | 1.69 | 74.5 | 0.466 | 0.637 | 1.5 | 1.4 | 3556 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | 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 | In house model | 1.6 | 48.8 | 1 | 127198 | 86732 | 4629 | 71.82 | 0.1889 | 0.1869 | 0.22616 | RANDOM | 16.45 | ||||
| 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] | |
| 0.79 | 0.79 | -1.57 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.628 |
| r_dihedral_angle_4_deg | 16.728 |
| r_dihedral_angle_3_deg | 13.395 |
| r_dihedral_angle_1_deg | 5.655 |
| r_scangle_it | 1.779 |
| r_angle_other_deg | 1.324 |
| r_scbond_it | 1.241 |
| r_angle_refined_deg | 1.184 |
| r_mcangle_it | 0.756 |
| r_mcbond_it | 0.692 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6532 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 747 |
| Heterogen Atoms | 77 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| ADSC | data collection |
| MOSFLM | data reduction |
| AMoRE | phasing |
