3REK

2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KX4 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5651.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.001α = 90
b = 109.436β = 90
c = 176.357γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.07SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.65793.50.06118.44.557610

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 REPLACEMENTTHROUGHOUT1KX42.65757610121093.080.260460.259990.2812RANDOM90.86
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]
2.58-3.931.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.277
r_dihedral_angle_4_deg18.983
r_dihedral_angle_3_deg18.52
r_dihedral_angle_1_deg5.098
r_scangle_it2.159
r_angle_refined_deg1.433
r_mcangle_it1.38
r_scbond_it1.215
r_mcbond_it0.808
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.277
r_dihedral_angle_4_deg18.983
r_dihedral_angle_3_deg18.52
r_dihedral_angle_1_deg5.098
r_scangle_it2.159
r_angle_refined_deg1.433
r_mcangle_it1.38
r_scbond_it1.215
r_mcbond_it0.808
r_nbtor_refined0.309
r_nbd_refined0.211
r_symmetry_vdw_refined0.193
r_symmetry_hbond_refined0.193
r_xyhbond_nbd_refined0.175
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6015
Nucleic Acid Atoms5980
Solvent Atoms
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement