6QT2
Radiation damage study on a 16mer DNA segment, structure at 6.2 MGy dose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6QT1 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.6 | 292 | 2 microliter 1.5 mM DNA solution (5mM HEPES pH 6.6) plus 2 microliter 10 mM HEPES pH 6.6 plus 4 microliter reservoir solution, against a reservoir of 1 ml 34% PEG200, 600 mM CaCl2 and 10 mM HEPES pH 8.6. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.16 | 43.14 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 36.864 | α = 90 |
b = 36.864 | β = 90 |
c = 162.063 | γ = 120 |
Symmetry | |
---|---|
Space Group | H 3 2 |
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 6M | 2018-10-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.8 | 31.34 | 92.5 | 0.056 | 0.068 | 0.038 | 0.996 | 8.7 | 3 | 3879 |
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 | 1.8 | 1.85 | 60 | 1.044 | 1.288 | 0.739 | 0.318 | 2.5 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 6QT1 | 1.8 | 31.34 | 3693 | 184 | 91.55 | 0.2227 | 0.2199 | 0.2819 | RANDOM | 50.011 |
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] | |
0.87 | 0.44 | 0.87 | -2.83 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_angle_refined_deg | 1.764 |
r_angle_other_deg | 1.688 |
r_chiral_restr | 0.084 |
r_gen_planes_refined | 0.023 |
r_bond_refined_d | 0.01 |
r_gen_planes_other | 0.003 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 325 |
Solvent Atoms | 40 |
Heterogen Atoms | 6 |
Software
Software | |
---|---|
Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
MOLREP | phasing |