3UQ8
Structure of adenylation domain of Haemophilus influenzae DNA ligases bound to NAD+ in adenylated state.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | The reservoir solution contained 16% (w/v) polyethylene glycol (PEG) 3500 and 350 mM sodium potassium tartrate. Hanging drops were set up at 18 C by mixing 2 l of protein solution with 2 l of the reservoir solution and crystals were observed within 3-4 days. , pH 7.5, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.75 | 55.27 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 70.233 | α = 90 |
b = 70.233 | β = 90 |
c = 161.286 | γ = 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 | 298 | CCD | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.933 | ESRF | ID14-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.7 | 32.2 | 90.69 | 41079 | 20 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.7 | 32.2 | 41079 | 2070 | 90.65 | 0.1868 | 0.1852 | 0.2162 | RANDOM | 14.6855 |
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] | |
-0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.212 |
r_dihedral_angle_4_deg | 14.549 |
r_dihedral_angle_3_deg | 12.088 |
r_dihedral_angle_1_deg | 5.692 |
r_scangle_it | 5.203 |
r_scbond_it | 3.343 |
r_mcangle_it | 2.06 |
r_angle_refined_deg | 2.021 |
r_mcbond_it | 1.222 |
r_chiral_restr | 0.155 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2551 |
Nucleic Acid Atoms | |
Solvent Atoms | 273 |
Heterogen Atoms | 66 |
Software
Software | |
---|---|
Software Name | Purpose |
MOSFLM | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
SCALA | data scaling |
AMoRE | phasing |