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Structural Insights into the Tumor Suppressor ZMYND11 Reveal Diverse Recognition Mechanisms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 40 % v/v 2-Methyl-2,4-pentanediol,100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.022 α = 90 b = 55.022 β = 90 c = 74.411 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 198 PIXEL DECTRIS EIGER X 16M 2022-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9793 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.628 47.76 99.88 0.997 73.4 19 8809
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.66 0.997
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING THROUGHOUT 1.628 47.65 8809 430 99.447 0.183 0.1809 0.181 0.2265 0.2266 RANDOM 46.074
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] 1.102 0.551 1.102 -3.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.652 r_dihedral_angle_4_deg 16.629 r_dihedral_angle_3_deg 14.94 r_scangle_it 8.428 r_scangle_other 8.424 r_lrange_other 8.061 r_lrange_it 8.033 r_mcangle_it 7.907 r_mcangle_other 7.894 r_scbond_it 7.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.652 r_dihedral_angle_4_deg 16.629 r_dihedral_angle_3_deg 14.94 r_scangle_it 8.428 r_scangle_other 8.424 r_lrange_other 8.061 r_lrange_it 8.033 r_mcangle_it 7.907 r_mcangle_other 7.894 r_scbond_it 7.279 r_scbond_other 7.262 r_dihedral_angle_1_deg 7.106 r_mcbond_it 6.443 r_mcbond_other 6.313 r_rigid_bond_restr 3.707 r_angle_refined_deg 1.561 r_angle_other_deg 0.619 r_symmetry_xyhbond_nbd_refined 0.263 r_symmetry_nbd_other 0.207 r_symmetry_nbd_refined 0.203 r_nbd_refined 0.191 r_nbtor_refined 0.191 r_nbd_other 0.139 r_chiral_restr 0.102 r_xyhbond_nbd_refined 0.094 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 422 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing