5T3L

B-DNA (CGCGAATTCGCG)2 soaked with selenourea for 1 min


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293Precipitant: 40 mM sodium cacodylate pH 7.0, 12 mM spermine tetrachloride, 80 mM NaCl, 10%(v/v) MPD; Well solution: 35% (v/v) MPD
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 24.384α = 90
b = 41.479β = 90
c = 65.996γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.979APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.58501000.13821.913.28220
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.641001.3072.110.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.5825.82779342784.70.150.1480.186RANDOM16.34
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]
-0.48-0.370.85
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.809
r_sphericity_bonded13.061
r_long_range_B_refined4.938
r_scangle_other4.432
r_long_range_B_other4.141
r_scbond_it3.429
r_scbond_other3.426
r_rigid_bond_restr3.254
r_angle_other_deg1.737
r_angle_refined_deg1.665
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.809
r_sphericity_bonded13.061
r_long_range_B_refined4.938
r_scangle_other4.432
r_long_range_B_other4.141
r_scbond_it3.429
r_scbond_other3.426
r_rigid_bond_restr3.254
r_angle_other_deg1.737
r_angle_refined_deg1.665
r_chiral_restr0.09
r_gen_planes_refined0.03
r_bond_refined_d0.01
r_bond_other_d0.004
r_gen_planes_other0.004
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms486
Solvent Atoms111
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing