5XF3

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29135-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.5952.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.19α = 90
b = 109.4β = 90
c = 174.82γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDPSI PILATUS 6M2014-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.5SLSX06DA

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
12.658.2799.9155.864455
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)
12.62.6799.60.5055.4

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 REPLACEMENTTHROUGHOUT3MNN2.652.74863050130399.80.235340.234580.27017RANDOM105.554
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]
9.65-7.35-2.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.454
r_dihedral_angle_4_deg20.623
r_dihedral_angle_3_deg17.142
r_long_range_B_refined16.016
r_long_range_B_other16.015
r_scangle_other11.892
r_mcangle_it8.156
r_mcangle_other8.155
r_scbond_it7.899
r_scbond_other7.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.454
r_dihedral_angle_4_deg20.623
r_dihedral_angle_3_deg17.142
r_long_range_B_refined16.016
r_long_range_B_other16.015
r_scangle_other11.892
r_mcangle_it8.156
r_mcangle_other8.155
r_scbond_it7.899
r_scbond_other7.895
r_dihedral_angle_1_deg5.761
r_mcbond_it5.707
r_mcbond_other5.699
r_angle_refined_deg1.452
r_angle_other_deg1.292
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms6094
Nucleic Acid Atoms5939
Solvent Atoms
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement