5XF4

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-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
2.5952.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.76α = 90
b = 109.56β = 90
c = 175.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDPSI PILATUS 6M2014-10-10MSINGLE 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
12.8770.3699.815.65.748120
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)
12.873.0399.10.4985.3

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 REPLACEMENTTHROUGHOUT3MNN2.8768.4234707198199.780.227740.226910.26574RANDOM110.569
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]
9.54-8.44-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.396
r_dihedral_angle_4_deg20.478
r_dihedral_angle_3_deg17.177
r_long_range_B_refined15.144
r_long_range_B_other15.143
r_scangle_other10.968
r_mcangle_it8.162
r_mcangle_other8.161
r_scbond_it7.105
r_scbond_other7.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.396
r_dihedral_angle_4_deg20.478
r_dihedral_angle_3_deg17.177
r_long_range_B_refined15.144
r_long_range_B_other15.143
r_scangle_other10.968
r_mcangle_it8.162
r_mcangle_other8.161
r_scbond_it7.105
r_scbond_other7.1
r_dihedral_angle_1_deg5.588
r_mcbond_it5.467
r_mcbond_other5.462
r_angle_refined_deg1.413
r_angle_other_deg1.272
r_chiral_restr0.195
r_bond_refined_d0.007
r_bond_other_d0.005
r_gen_planes_refined0.005
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 Atoms6094
Nucleic Acid Atoms5939
Solvent Atoms
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement