6BJI
Human ABO(H) blood group glycosyltransferase GTA D302C mutant
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1LZ0 | PDB entry 1LZ0 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | SMALL TUBES | 277 | Spontaneous crystals were recovered from concentrated stocks of GTA/D302C (95-100 mg/mL) stored in 50 mM MOPS, pH 7.00, 0.1 M sodium chloride, 1 mM DTT, 5 mM manganese chloride, and kept at 277 K. | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.28 | 46.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.58 | α = 90 |
| b = 149.57 | β = 90 |
| c = 79.56 | 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 | 113 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2006-11-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SEALED TUBE | RIGAKU | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.54 | 19.79 | 98.7 | 0.038 | 0.038 | 17.2 | 4.44 | 46171 | |||||||||||
| 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 | 1.54 | 1.6 | 100 | 0.32 | 3.3 | 3.61 | |||||||||||||
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 1LZ0 | 1.54 | 19.79 | 43837 | 2329 | 98.58 | 0.1824 | 0.1811 | 0.2087 | RANDOM | 21.503 | ||||||
| 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] | |
| -0.26 | 0.6 | -0.35 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.663 |
| r_dihedral_angle_4_deg | 16.525 |
| r_dihedral_angle_3_deg | 11.867 |
| r_dihedral_angle_1_deg | 6.477 |
| r_angle_refined_deg | 1.411 |
| r_angle_other_deg | 0.958 |
| r_chiral_restr | 0.085 |
| r_bond_refined_d | 0.009 |
| r_gen_planes_refined | 0.007 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2238 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 270 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| d*TREK | data scaling |
| PDB_EXTRACT | data extraction |
| CrystalClear | data reduction |
| MOLREP | phasing |
