5U8A

Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K0M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52903.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5
Crystal Properties
Matthews coefficientSolvent content
2.6253.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.768α = 90
b = 85.142β = 90
c = 91.443γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.4591.4431000.0710.99916.86.580241
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.4521.45799.70.9060.7282.16.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5K0M1.4562.3176142402199.890.152030.150940.17318RANDOM15.084
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]
0.48-0.530.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.795
r_dihedral_angle_4_deg20.319
r_sphericity_free13.933
r_dihedral_angle_3_deg12.488
r_dihedral_angle_1_deg6.542
r_sphericity_bonded3.188
r_long_range_B_refined1.722
r_long_range_B_other1.562
r_rigid_bond_restr1.557
r_angle_refined_deg1.475
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.795
r_dihedral_angle_4_deg20.319
r_sphericity_free13.933
r_dihedral_angle_3_deg12.488
r_dihedral_angle_1_deg6.542
r_sphericity_bonded3.188
r_long_range_B_refined1.722
r_long_range_B_other1.562
r_rigid_bond_restr1.557
r_angle_refined_deg1.475
r_scbond_it1.422
r_scbond_other1.421
r_scangle_other1.421
r_angle_other_deg0.961
r_mcangle_other0.957
r_mcangle_it0.956
r_mcbond_it0.816
r_mcbond_other0.812
r_chiral_restr0.091
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2898
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing