3F9Y

Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZKKPDB entry 1ZKK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529825% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.4α = 91.4
b = 45β = 115.3
c = 52.4γ = 89.8
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 300 mm CCD2006-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.5250.06722.57.8559072
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.60.5288.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1ZKK1.523.6825340728111000.194970.193640.22012RANDOM32.444
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]
-0.25-0.050.10.210.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.569
r_dihedral_angle_4_deg17.717
r_dihedral_angle_3_deg14.017
r_dihedral_angle_1_deg6.543
r_scangle_it4.082
r_scbond_it2.794
r_angle_refined_deg1.895
r_mcangle_it1.862
r_mcbond_it1.216
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.569
r_dihedral_angle_4_deg17.717
r_dihedral_angle_3_deg14.017
r_dihedral_angle_1_deg6.543
r_scangle_it4.082
r_scbond_it2.794
r_angle_refined_deg1.895
r_mcangle_it1.862
r_mcbond_it1.216
r_nbtor_refined0.308
r_symmetry_vdw_refined0.235
r_nbd_refined0.217
r_symmetry_hbond_refined0.205
r_xyhbond_nbd_refined0.159
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2680
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms52

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling