3IJ0

Crystal structure of Eed in complex with a trimethylated histone H3K9 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
2.5852.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.583α = 90
b = 85.087β = 90
c = 91.266γ = 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
12.455095.50.1170.1179.94.116201162012
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)
2.452.5497.80.3520.3523.14

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 structure2.4550154721547283495.560.184280.184280.181110.24412RANDOM16.974
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]
0.19-1.160.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.972
r_dihedral_angle_4_deg15.782
r_dihedral_angle_3_deg14.081
r_dihedral_angle_1_deg6.698
r_scangle_it2.204
r_scbond_it1.323
r_angle_refined_deg1.287
r_mcangle_it0.916
r_mcbond_it0.521
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.972
r_dihedral_angle_4_deg15.782
r_dihedral_angle_3_deg14.081
r_dihedral_angle_1_deg6.698
r_scangle_it2.204
r_scbond_it1.323
r_angle_refined_deg1.287
r_mcangle_it0.916
r_mcbond_it0.521
r_nbtor_refined0.303
r_nbd_refined0.187
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.135
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2944
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms

Software

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