8YTI

Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UT9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29140-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Crystal Properties
Matthews coefficientSolvent content
2.4349.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.852α = 90
b = 102.111β = 96.337
c = 216.179γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98PIXELDECTRIS PILATUS 2M-F2015-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.792.2299.60.9989.83.4124272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.850.521

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.792.22124251240299.5620.2110.20960.266988.021
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]
-2.5760.622-1.2863.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.684
r_dihedral_angle_3_deg19.796
r_dihedral_angle_4_deg18.479
r_lrange_it10.573
r_lrange_other10.567
r_scangle_it7.637
r_scangle_other7.637
r_dihedral_angle_1_deg6.598
r_mcangle_it6.48
r_mcangle_other6.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.684
r_dihedral_angle_3_deg19.796
r_dihedral_angle_4_deg18.479
r_lrange_it10.573
r_lrange_other10.567
r_scangle_it7.637
r_scangle_other7.637
r_dihedral_angle_1_deg6.598
r_mcangle_it6.48
r_mcangle_other6.48
r_scbond_it4.929
r_scbond_other4.929
r_mcbond_it4.192
r_mcbond_other4.191
r_angle_other_deg1.334
r_angle_refined_deg1.229
r_symmetry_nbd_refined0.285
r_nbd_other0.271
r_symmetry_xyhbond_nbd_refined0.233
r_symmetry_nbd_other0.213
r_nbtor_refined0.204
r_metal_ion_refined0.203
r_nbd_refined0.186
r_xyhbond_nbd_refined0.165
r_symmetry_metal_ion_refined0.152
r_symmetry_nbtor_other0.075
r_symmetry_xyhbond_nbd_other0.069
r_chiral_restr0.066
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14012
Nucleic Acid Atoms13846
Solvent Atoms157
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing