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Crystal structure of the methyl-CpG-binding domain of SETDB2 in complex with the cysteine-rich domain of C11orf46 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house model (SAD-phased)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 2.0 M ammonium sulfate
0.1 M Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.97 α = 90 b = 69.97 β = 90 c = 116.88 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS EIGER X 9M 2020-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.82 42.06 99.8 0.098 0.026 0.999 15.8 13.1 30318
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 96.8 0.898 0.294 0.812 2.3 8.6
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 in-house model (SAD-phased) 1.82 42.06 28818 1468 99.73 0.18812 0.18615 0.1938 0.22662 0.2349 RANDOM 34.278
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] 0.14 0.07 0.14 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.425 r_dihedral_angle_4_deg 25.341 r_dihedral_angle_3_deg 13.726 r_long_range_B_refined 8.419 r_long_range_B_other 8.404 r_dihedral_angle_1_deg 8.092 r_scangle_other 6.506 r_mcangle_it 4.611 r_mcangle_other 4.61 r_scbond_it 4.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.425 r_dihedral_angle_4_deg 25.341 r_dihedral_angle_3_deg 13.726 r_long_range_B_refined 8.419 r_long_range_B_other 8.404 r_dihedral_angle_1_deg 8.092 r_scangle_other 6.506 r_mcangle_it 4.611 r_mcangle_other 4.61 r_scbond_it 4.318 r_scbond_other 4.21 r_mcbond_it 3.306 r_mcbond_other 3.292 r_angle_refined_deg 1.678 r_angle_other_deg 1.375 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2422 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Coot model building BUCCANEER model building SHELXCD phasing Aimless data scaling XDS data reduction