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Crystal structure of YEATS2 YEATS domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Tris-HCl buffer (pH 8.5) containing 2 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.2 61.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.448 α = 90 b = 50.84 β = 100.22 c = 82.629 γ = 90
Symmetry Space Group C 1 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 CCD RAYONIX MX225HE 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.67 50 100 0.044 11.6 3.8 43069
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 0.746
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 4TMP 1.67 44.55 41299 1769 100 0.17487 0.1737 0.1794 0.2019 0.2059 RANDOM 36.867
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] -0.52 -0.22 1.24 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_4_deg 11.675 r_dihedral_angle_3_deg 10.509 r_dihedral_angle_1_deg 6.015 r_long_range_B_refined 3.774 r_long_range_B_other 3.448 r_scangle_other 2.658 r_mcangle_other 2.494 r_mcangle_it 2.487 r_scbond_it 2.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_4_deg 11.675 r_dihedral_angle_3_deg 10.509 r_dihedral_angle_1_deg 6.015 r_long_range_B_refined 3.774 r_long_range_B_other 3.448 r_scangle_other 2.658 r_mcangle_other 2.494 r_mcangle_it 2.487 r_scbond_it 2.016 r_scbond_other 2.015 r_mcbond_other 1.775 r_mcbond_it 1.773 r_angle_refined_deg 1.14 r_angle_other_deg 1.12 r_rigid_bond_restr 0.788 r_chiral_restr 0.047 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 2050 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing