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Study on the structure and function of tumor suppressor ZMYND11
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 (Observed) 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 1.63 47.65 8372 437 99.45 0.17358 0.17336 0.1776 0.17784 0.1877 RANDOM 46.185
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] 1.13 0.56 1.13 -3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.116 r_dihedral_angle_4_deg 16.325 r_dihedral_angle_3_deg 15.1 r_scangle_other 9.59 r_long_range_B_other 8.474 r_long_range_B_refined 8.446 r_mcangle_it 8.04 r_mcangle_other 8.025 r_scbond_it 7.756 r_scbond_other 7.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.116 r_dihedral_angle_4_deg 16.325 r_dihedral_angle_3_deg 15.1 r_scangle_other 9.59 r_long_range_B_other 8.474 r_long_range_B_refined 8.446 r_mcangle_it 8.04 r_mcangle_other 8.025 r_scbond_it 7.756 r_scbond_other 7.738 r_dihedral_angle_1_deg 6.99 r_mcbond_it 6.791 r_mcbond_other 6.697 r_rigid_bond_restr 3.997 r_angle_refined_deg 1.587 r_angle_other_deg 0.632 r_chiral_restr 0.105 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 420 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing