3REJ

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6291pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5852.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.067α = 90
b = 109.374β = 90
c = 176.465γ = 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
12.559391.60.07917.56.560540

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 REPLACEMENTTHROUGHOUT1KX42.5592.8560540125391.390.23430.233720.2624RANDOM70.538
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]
0.47-1.771.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.091
r_dihedral_angle_4_deg19.075
r_dihedral_angle_3_deg18.408
r_dihedral_angle_1_deg5.175
r_scangle_it2.023
r_angle_refined_deg1.432
r_mcangle_it1.285
r_scbond_it1.138
r_mcbond_it0.729
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.091
r_dihedral_angle_4_deg19.075
r_dihedral_angle_3_deg18.408
r_dihedral_angle_1_deg5.175
r_scangle_it2.023
r_angle_refined_deg1.432
r_mcangle_it1.285
r_scbond_it1.138
r_mcbond_it0.729
r_nbtor_refined0.31
r_symmetry_vdw_refined0.213
r_nbd_refined0.212
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.176
r_chiral_restr0.074
r_symmetry_metal_ion_refined0.043
r_bond_refined_d0.009
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_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 Atoms390
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement