5JU4

Crystal structure of a DNA sequence d(CGTGAATTCACG) at 130K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D29 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29360mM Sodium cacodylate, 17mM MgCl2, 2m M Spermine, 50% MPD, 1.5mM DAPI
Crystal Properties
Matthews coefficientSolvent content
2.2445.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 24.503α = 90
b = 41.09β = 90
c = 65.184γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130CCDAGILENT ATLAS CCD2016-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.54

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
1214.899.50.07518.73.94550
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)
122.070.368

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1D29234.76452425099.540.22260.218640.29214RANDOM31.01
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]
1.540.65-2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined7.142
r_long_range_B_other6.484
r_scangle_other4.801
r_scbond_it3.37
r_scbond_other3.368
r_angle_other_deg1.819
r_angle_refined_deg1.776
r_chiral_restr0.081
r_gen_planes_refined0.02
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined7.142
r_long_range_B_other6.484
r_scangle_other4.801
r_scbond_it3.37
r_scbond_other3.368
r_angle_other_deg1.819
r_angle_refined_deg1.776
r_chiral_restr0.081
r_gen_planes_refined0.02
r_bond_refined_d0.009
r_bond_other_d0.004
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms486
Solvent Atoms56
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing