3IIY

Crystal structure of Eed in complex with a trimethylated histone H1K26 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSeMet Eed Structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82914M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5952.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.573α = 90
b = 85.18β = 90
c = 91.352γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.653098.10.1190.11911.34.212915129152
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.652.7498.80.3890.3893.24

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSeMet Eed Structure2.6530126701267065998.240.184180.184180.180360.25924RANDOM17.696
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]
0.14-1.321.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.391
r_dihedral_angle_4_deg16.19
r_dihedral_angle_3_deg15.05
r_dihedral_angle_1_deg6.442
r_scangle_it1.876
r_angle_refined_deg1.215
r_scbond_it1.085
r_mcangle_it0.914
r_mcbond_it0.498
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.391
r_dihedral_angle_4_deg16.19
r_dihedral_angle_3_deg15.05
r_dihedral_angle_1_deg6.442
r_scangle_it1.876
r_angle_refined_deg1.215
r_scbond_it1.085
r_mcangle_it0.914
r_mcbond_it0.498
r_nbtor_refined0.305
r_symmetry_hbond_refined0.235
r_nbd_refined0.189
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.141
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3000
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling