5MVU
Crystal structure of an A-DNA dodecamer containing 5-formylcytosine in 3 consecutive CpG steps
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Magnesium chloride (18 mM) Spermine tetrahydrochloride (3 mM) Sodium cacodylate (50 mM) 2-Propanol (10% v/v) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.32 | 47 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 44.2 | α = 90 |
b = 44.2 | β = 90 |
c = 61.683 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 32 2 1 |
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 | 2016-09-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976 | Diamond | I03 |
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 | 2.3 | 38.28 | 99.91 | 15.4 | 8.9 | 3349 |
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 | FREE R-VALUE | 5MVL | 2.3 | 32.52 | 3170 | 161 | 99.91 | 0.14921 | 0.14881 | 0.15756 | RANDOM | 63.078 |
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] | |
-3.75 | -3.75 | 7.51 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_long_range_B_refined | 9.477 |
r_long_range_B_other | 9.472 |
r_scangle_other | 8.382 |
r_scbond_other | 5.329 |
r_scbond_it | 5.328 |
r_angle_other_deg | 1.533 |
r_angle_refined_deg | 1.51 |
r_chiral_restr | 0.085 |
r_gen_planes_refined | 0.01 |
r_bond_refined_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 498 |
Solvent Atoms | 3 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |