☰ Navigation Tabs
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
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 = 57.768 α = 90 b = 85.142 β = 90 c = 91.443 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 2013-10-10 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 1.45 91.443 100 0.071 0.999 16.8 6.5 80241
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) Redundancy Number Unique Reflections (All) 1 1.452 1.457 99.7 0.906 0.728 2.1 6.7
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 1.45 62.31 76142 4021 99.89 0.15203 0.15094 0.151 0.17318 0.1731 RANDOM 15.084
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 -0.53 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.795 r_dihedral_angle_4_deg 20.319 r_sphericity_free 13.933 r_dihedral_angle_3_deg 12.488 r_dihedral_angle_1_deg 6.542 r_sphericity_bonded 3.188 r_long_range_B_refined 1.722 r_long_range_B_other 1.562 r_rigid_bond_restr 1.557 r_angle_refined_deg 1.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.795 r_dihedral_angle_4_deg 20.319 r_sphericity_free 13.933 r_dihedral_angle_3_deg 12.488 r_dihedral_angle_1_deg 6.542 r_sphericity_bonded 3.188 r_long_range_B_refined 1.722 r_long_range_B_other 1.562 r_rigid_bond_restr 1.557 r_angle_refined_deg 1.475 r_scbond_it 1.422 r_scbond_other 1.421 r_scangle_other 1.421 r_angle_other_deg 0.961 r_mcangle_other 0.957 r_mcangle_it 0.956 r_mcbond_it 0.816 r_mcbond_other 0.812 r_chiral_restr 0.091 r_bond_refined_d 0.009 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 226 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing