3SX3
Crystal structure of AABB+UDP+Gal with glycerol as the cryoprotectant
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1LZ7 | PDB ENTRY 1LZ7 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 298 | 1% PEG4000, 5% MPD, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, pH 7.6, 30 mM sodium acetate, pH 4.6, 5 mM manganese chloride, with 30% Glycerol as cryoprotectant, HANGING DROP, temperature 298K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.27 | 45.75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.39 | α = 90 |
| b = 149.12 | β = 90 |
| c = 79.46 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 RAXIS | OSMIC BLUE MIRRORS | 2007-11-28 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-002 | 1.54 | ||
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 | 1.45 | 74.536 | 96.3 | 0.042 | 16 | 4.27 | 53446 | ||||||||||||
| 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 | 1.45 | 1.5 | 96 | 0.371 | 3 | 3.48 | 5256 | ||||||||||||
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 1LZ7 | 1.45 | 20 | 53442 | 2703 | 96.27 | 0.1996 | 0.1981 | 0.2269 | RANDOM | 19.3385 | ||||||
| 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] | |
| -0.17 | 0.13 | 0.04 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.903 |
| r_dihedral_angle_4_deg | 18.569 |
| r_dihedral_angle_3_deg | 12.723 |
| r_dihedral_angle_1_deg | 6.556 |
| r_scangle_it | 5.099 |
| r_scbond_it | 3.678 |
| r_angle_refined_deg | 2.38 |
| r_mcangle_it | 2.312 |
| r_mcbond_it | 1.439 |
| r_chiral_restr | 0.164 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2394 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 260 |
| Heterogen Atoms | 51 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| d*TREK | data reduction |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CrystalClear | data collection |
| d*TREK | data scaling |
| MOLREP | phasing |
