5V0Z
Crystal structure of Galactoside O-acetyltransferase complex with CoA (P32 space group).
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5U2K |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289 | 1uL of 15 mg/ml protein incubated with 5mM CoA were mixed with 1 uL of 25% w/v PEG 3350, 250 mM Sodium/Potassium phosphate, 30% v/v Ethylene glycol and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.28 | 45.96 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 75.434 | α = 90 |
b = 75.434 | β = 90 |
c = 93.178 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 32 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 X 6M | 2016-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97857 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.26 | 50 | 99.4 | 0.04 | 0.048 | 0.027 | 6 | 2.9 | 159888 | 13.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.26 | 1.28 | 99.8 | 0.345 | 0.428 | 0.25 | 0.925 | 2.1 | 2.8 |
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 | 5U2K | 1.26 | 50 | 151162 | 8155 | 99.39 | 0.1375 | 0.1361 | 0.1642 | RANDOM | 19.58 |
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] | |
-0.16 | -0.08 | -0.16 | 0.52 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_sphericity_free | 35.372 |
r_dihedral_angle_2_deg | 35.086 |
r_sphericity_bonded | 16.461 |
r_dihedral_angle_4_deg | 15.267 |
r_dihedral_angle_3_deg | 11.098 |
r_dihedral_angle_1_deg | 6.072 |
r_rigid_bond_restr | 4.271 |
r_angle_refined_deg | 1.729 |
r_angle_other_deg | 1.204 |
r_chiral_restr | 0.118 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4428 |
Nucleic Acid Atoms | |
Solvent Atoms | 826 |
Heterogen Atoms | 355 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-3000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data collection |
HKL-3000 | phasing |
MOLREP | phasing |
SCALEPACK | data scaling |