☰ Navigation Tabs
Crystal structure of AF9 YEATS domain in complex with H4K8acK12ac peptide
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 293 200 mM ammonium citrate tribasic buffer (pH 7.0) containing 19% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.963 α = 84.86 b = 44.913 β = 86.09 c = 58.797 γ = 66.33
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 1.996 50 97.3 0.04 13.9 2 26432
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 2 2.03 0.316
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 2 39.36 24532 1274 95.21 0.20381 0.20245 0.2025 0.22881 0.2288 RANDOM 32.665
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] -0.17 0.34 0.09 0.41 -1.46 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.74 r_dihedral_angle_4_deg 13.163 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 5.916 r_long_range_B_refined 5.22 r_mcangle_it 2.174 r_scbond_it 1.493 r_mcbond_it 1.227 r_angle_refined_deg 0.79 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.74 r_dihedral_angle_4_deg 13.163 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 5.916 r_long_range_B_refined 5.22 r_mcangle_it 2.174 r_scbond_it 1.493 r_mcbond_it 1.227 r_angle_refined_deg 0.79 r_chiral_restr 0.061 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2426 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing