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Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 290 3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.047 α = 90 b = 85.4 β = 90 c = 91.977 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2013-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.28 62.58 99.8 0.077 9.8 5.9 118159
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.33 99.7 0.756 2.9 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K0M 1.28 62.58 111899 5912 99.74 0.13405 0.1331 0.1333 0.15211 0.1518 RANDOM 16.733
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] -0.22 0.01 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.853 r_sphericity_free 22.423 r_dihedral_angle_4_deg 14.904 r_dihedral_angle_3_deg 11.456 r_sphericity_bonded 8.053 r_rigid_bond_restr 7.632 r_dihedral_angle_1_deg 6.629 r_long_range_B_refined 3.533 r_long_range_B_other 3.533 r_scangle_other 3.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.853 r_sphericity_free 22.423 r_dihedral_angle_4_deg 14.904 r_dihedral_angle_3_deg 11.456 r_sphericity_bonded 8.053 r_rigid_bond_restr 7.632 r_dihedral_angle_1_deg 6.629 r_long_range_B_refined 3.533 r_long_range_B_other 3.533 r_scangle_other 3.257 r_scbond_it 2.743 r_scbond_other 2.742 r_angle_refined_deg 1.424 r_mcangle_it 1.345 r_mcangle_other 1.345 r_mcbond_it 1.056 r_angle_other_deg 0.996 r_mcbond_other 0.978 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2898 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing