5XF5

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29135-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.6854.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.21α = 90
b = 109.67β = 90
c = 182.04γ = 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
12.8270.6599.913.35.852474
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)
12.822.9799.60.5025.1

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 REPLACEMENTTHROUGHOUT3MNN2.8270.6551315108299.890.228470.22770.26351RANDOM97.989
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]
0.93-6.635.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.258
r_dihedral_angle_4_deg20.697
r_dihedral_angle_3_deg16.507
r_long_range_B_refined11.813
r_long_range_B_other11.813
r_scangle_other8.333
r_mcangle_it6.527
r_mcangle_other6.526
r_scbond_it5.406
r_scbond_other5.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.258
r_dihedral_angle_4_deg20.697
r_dihedral_angle_3_deg16.507
r_long_range_B_refined11.813
r_long_range_B_other11.813
r_scangle_other8.333
r_mcangle_it6.527
r_mcangle_other6.526
r_scbond_it5.406
r_scbond_other5.406
r_dihedral_angle_1_deg5.257
r_mcbond_it4.217
r_mcbond_other4.216
r_angle_other_deg1.253
r_angle_refined_deg1.197
r_chiral_restr0.069
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
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