8Q3X

Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6IPU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Crystal Properties
Matthews coefficientSolvent content
3.0659.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.105α = 90
b = 109.609β = 90
c = 183.767γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98PIXELDECTRIS PILATUS 2M-F2018-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.04SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.348.9399.9127.312.297275
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.430.651

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.30148.9397189195299.8320.2240.22350.2623394.074
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]
4.758-4.7840.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.82
r_dihedral_angle_4_deg21.142
r_dihedral_angle_3_deg18.892
r_lrange_it15.477
r_lrange_other15.477
r_scangle_it12.244
r_scangle_other12.243
r_mcangle_other8.629
r_mcangle_it8.628
r_scbond_it8.289
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.82
r_dihedral_angle_4_deg21.142
r_dihedral_angle_3_deg18.892
r_lrange_it15.477
r_lrange_other15.477
r_scangle_it12.244
r_scangle_other12.243
r_mcangle_other8.629
r_mcangle_it8.628
r_scbond_it8.289
r_scbond_other8.288
r_dihedral_angle_1_deg6.272
r_mcbond_it6.176
r_mcbond_other6.173
r_angle_other_deg2.441
r_angle_refined_deg1.474
r_symmetry_nbd_other0.242
r_symmetry_xyhbond_nbd_refined0.21
r_nbtor_refined0.207
r_nbd_refined0.205
r_nbd_other0.198
r_symmetry_nbd_refined0.155
r_xyhbond_nbd_refined0.144
r_chiral_restr0.083
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.076
r_bond_other_d0.028
r_gen_planes_other0.013
r_gen_planes_refined0.008
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6215
Nucleic Acid Atoms5939
Solvent Atoms
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing