3IIW

Crystal structure of Eed in complex with a trimethylated histone H3K27 peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82914.0 M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5952.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.745α = 90
b = 85.118β = 90
c = 91.246γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Kirkpatrick-Baez bimorph mirror pair for horizontal and vertical focusingMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9700DiamondI04

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
11.83097.80.0730.07711.33.740269220.37
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)
1.81.8885.80.2790.3032.82.4

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 structure1.8303938339383208497.810.158960.158960.157110.19315RANDOM21.888
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]
0.32-0.710.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.529
r_dihedral_angle_4_deg17.09
r_dihedral_angle_3_deg13.755
r_dihedral_angle_1_deg7.134
r_scangle_it6.58
r_scbond_it4.225
r_mcangle_it2.837
r_mcbond_it1.716
r_angle_refined_deg1.486
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.529
r_dihedral_angle_4_deg17.09
r_dihedral_angle_3_deg13.755
r_dihedral_angle_1_deg7.134
r_scangle_it6.58
r_scbond_it4.225
r_mcangle_it2.837
r_mcbond_it1.716
r_angle_refined_deg1.486
r_chiral_restr0.139
r_gen_planes_refined0.016
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2943
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms

Software

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