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Targeting the PRC2 complex through a novel protein-protein interaction inhibitor of EED
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JZN
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 = 57.843 α = 90 b = 84.911 β = 90 c = 91.627 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 PIXEL DECTRIS PILATUS 6M 2016-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.828 48.92 100 0.141 0.997 12.7 6.4 40632
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 1.828 1.834 98.6 1.145 2 6.4
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 3JZN 1.83 48.912 38572 1997 99.78 0.13598 0.13344 0.1463 0.18475 0.1942 RANDOM 23.309
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] -0.69 0.09 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.369 r_sphericity_free 34.854 r_dihedral_angle_4_deg 16.325 r_dihedral_angle_3_deg 11.74 r_rigid_bond_restr 9.442 r_sphericity_bonded 7.925 r_dihedral_angle_1_deg 6.618 r_long_range_B_refined 4.486 r_long_range_B_other 3.706 r_scangle_other 2.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.369 r_sphericity_free 34.854 r_dihedral_angle_4_deg 16.325 r_dihedral_angle_3_deg 11.74 r_rigid_bond_restr 9.442 r_sphericity_bonded 7.925 r_dihedral_angle_1_deg 6.618 r_long_range_B_refined 4.486 r_long_range_B_other 3.706 r_scangle_other 2.943 r_scbond_it 2.812 r_scbond_other 2.811 r_mcangle_it 1.953 r_mcangle_other 1.952 r_mcbond_it 1.587 r_mcbond_other 1.587 r_angle_refined_deg 1.427 r_angle_other_deg 1.239 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2906 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing