2HIX
ATP dependent DNA ligase from S. solfataricus bound to ATP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 298 | 6-8% PEG 3350, 50 mM sodium acetate pH 4.5, 30-80 mM sodium/potassium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.97 | 58.57 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 119.324 | α = 90 |
b = 171.65 | β = 90 |
c = 78.686 | 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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 12.3.1 | ALS | 12.3.1 |
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 | 2.86 | 50 | 96.4 | 0.077 | 14.4 | 3.9 | 18026 | 18026 |
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 | 2.86 | 3 | 84.5 | 0.349 | 3.2 | 1570 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.87 | 20 | 17962 | 17962 | 916 | 94.98 | 0.221 | 0.217 | 0.217 | 0.2 | 0.279 | 0.26 | RANDOM | 49.765 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-1.99 | -2.33 | 4.32 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.939 |
r_dihedral_angle_4_deg | 21.789 |
r_dihedral_angle_3_deg | 19.69 |
r_dihedral_angle_1_deg | 5.638 |
r_scangle_it | 1.769 |
r_angle_refined_deg | 1.338 |
r_scbond_it | 1.054 |
r_mcangle_it | 0.747 |
r_mcbond_it | 0.414 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4562 |
Nucleic Acid Atoms | |
Solvent Atoms | 4 |
Heterogen Atoms | 31 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |