5XF6

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29140 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.754.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.84α = 90
b = 109.729β = 90
c = 182.527γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDPSI PILATUS 6M2013-09-08MSINGLE 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
12.6348.8194.531.85.360682
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.632.7771.62.4

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 REPLACEMENTTHROUGHOUT3MNN2.6347.1557584303294.240.21050.20820.25422RANDOM90.39
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]
2.39-4.822.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_4_deg22.052
r_dihedral_angle_3_deg17.82
r_long_range_B_refined13.517
r_long_range_B_other13.517
r_scangle_other10.047
r_scbond_it6.729
r_scbond_other6.729
r_mcangle_it6.65
r_mcangle_other6.649
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_4_deg22.052
r_dihedral_angle_3_deg17.82
r_long_range_B_refined13.517
r_long_range_B_other13.517
r_scangle_other10.047
r_scbond_it6.729
r_scbond_other6.729
r_mcangle_it6.65
r_mcangle_other6.649
r_dihedral_angle_1_deg5.429
r_mcbond_it4.477
r_mcbond_other4.475
r_angle_refined_deg1.454
r_angle_other_deg1.201
r_chiral_restr0.211
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms6086
Nucleic Acid Atoms5939
Solvent Atoms22
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement