5CP6

Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WU8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629140 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7254.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.57α = 90
b = 109.57β = 90
c = 182.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98PIXELPSI PILATUS 6M2013-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.50SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.676.3986.315.14.857728

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 REPLACEMENTTHROUGHOUT4WU82.676.3956191115986.320.211020.210150.25064RANDOM84.143
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]
4.31-5.040.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.743
r_dihedral_angle_4_deg23.395
r_dihedral_angle_3_deg18.79
r_long_range_B_refined13.05
r_long_range_B_other13.049
r_scangle_other9.801
r_mcangle_it6.683
r_mcangle_other6.682
r_scbond_it6.664
r_scbond_other6.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.743
r_dihedral_angle_4_deg23.395
r_dihedral_angle_3_deg18.79
r_long_range_B_refined13.05
r_long_range_B_other13.049
r_scangle_other9.801
r_mcangle_it6.683
r_mcangle_other6.682
r_scbond_it6.664
r_scbond_other6.663
r_dihedral_angle_1_deg6.081
r_mcbond_it4.527
r_mcbond_other4.526
r_angle_refined_deg1.446
r_angle_other_deg1.365
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms6064
Nucleic Acid Atoms5939
Solvent Atoms35
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling