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Crystal Structure of chromodomain of CBX8 in complex with inhibitor UNC3866
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.4 M sodium citrate, 0.1 M HEPES, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.575 α = 90 b = 30.007 β = 100.17 c = 36.104 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315 2014-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9786036 APS 19-ID
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 1.18 35.54 99.5 0.038 20.5 3.5 21328
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 1.18 1.2 94.5 0.343 3.7 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.18 35.54 20239 1069 99.5 0.158 0.156 0.1689 0.186 0.1999 11.56
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] -0.02 0.18 -0.26 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.544 r_sphericity_free 21.278 r_dihedral_angle_4_deg 13.716 r_dihedral_angle_3_deg 9.976 r_sphericity_bonded 8.892 r_dihedral_angle_1_deg 6.317 r_rigid_bond_restr 2.877 r_angle_refined_deg 1.96 r_mcangle_it 1.777 r_mcbond_it 1.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.544 r_sphericity_free 21.278 r_dihedral_angle_4_deg 13.716 r_dihedral_angle_3_deg 9.976 r_sphericity_bonded 8.892 r_dihedral_angle_1_deg 6.317 r_rigid_bond_restr 2.877 r_angle_refined_deg 1.96 r_mcangle_it 1.777 r_mcbond_it 1.257 r_mcbond_other 1.255 r_angle_other_deg 1.098 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.003 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 525 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing