3LZ0

Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KX4NCP146b (pdb code 1KX4)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6291K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6453.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.37α = 90
b = 109.66β = 90
c = 175.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELPSI PILATUS 6M2009-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.593.0490.60.087.84.66550965509
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6461.90.3840.3841.92.16362

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNCP146b (pdb code 1KX4)2.593.0465180131789.970.2680.2690.2680.318RANDOM109.277
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]
7.93-7.46-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.721
r_dihedral_angle_3_deg20.849
r_dihedral_angle_4_deg18.838
r_dihedral_angle_1_deg5.835
r_scangle_it1.634
r_angle_refined_deg1.453
r_mcangle_it1.139
r_scbond_it0.901
r_mcbond_it0.635
r_symmetry_hbond_refined0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.721
r_dihedral_angle_3_deg20.849
r_dihedral_angle_4_deg18.838
r_dihedral_angle_1_deg5.835
r_scangle_it1.634
r_angle_refined_deg1.453
r_mcangle_it1.139
r_scbond_it0.901
r_mcbond_it0.635
r_symmetry_hbond_refined0.37
r_nbtor_refined0.31
r_symmetry_vdw_refined0.232
r_nbd_refined0.224
r_xyhbond_nbd_refined0.168
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5959
Nucleic Acid Atoms5939
Solvent Atoms
Heterogen Atoms10

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASESphasing