6JXD

Human nucleosome core particle with cohesive end DNA termini


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NZD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6291.15manganese chloride, potassium chloride, potassium cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.9858.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.31α = 90
b = 109.66β = 90
c = 183.819γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98.15PIXELDECTRIS PILATUS 2M-F2017-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.2594.1899.70.030.99712.211.5101214
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.370.76

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 REPLACEMENTTHROUGHOUT2NZD2.2592.0899086202299.60.239750.238680.29225RANDOM78.326
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]
5.45-5.50.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.331
r_dihedral_angle_3_deg19.571
r_dihedral_angle_4_deg18.65
r_long_range_B_refined13.424
r_long_range_B_other13.424
r_scangle_other10.415
r_mcangle_it7.355
r_mcangle_other7.354
r_scbond_it7.245
r_scbond_other7.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.331
r_dihedral_angle_3_deg19.571
r_dihedral_angle_4_deg18.65
r_long_range_B_refined13.424
r_long_range_B_other13.424
r_scangle_other10.415
r_mcangle_it7.355
r_mcangle_other7.354
r_scbond_it7.245
r_scbond_other7.245
r_dihedral_angle_1_deg6.379
r_mcbond_it5.08
r_mcbond_other5.08
r_angle_refined_deg1.496
r_angle_other_deg1.458
r_chiral_restr0.08
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6129
Nucleic Acid Atoms6029
Solvent Atoms52
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing