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Arabidopsis thaliana Histone deacetylase 7 (HDA7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 0.1M HEPES, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.83 32.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.308 α = 90 b = 74.475 β = 112.02 c = 47.59 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 2M 2021-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9794 ESRF ID23-2
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 1.5 43.9 98.1 0.93 9.7 7.2 47979
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 1.5 1.53 96.8 0.703 3.2 7.9
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 MOLECULAR REPLACEMENT THROUGHOUT 1.5 43.9 45496 2458 97.9 0.15922 0.15715 0.1603 0.19929 0.2015 RANDOM 14.675
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] 1.69 0.46 -1.34 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.377 r_dihedral_angle_2_deg 8.691 r_dihedral_angle_1_deg 6.296 r_rigid_bond_restr 3.164 r_long_range_B_refined 2.124 r_long_range_B_other 2.054 r_angle_refined_deg 1.542 r_scangle_other 1.408 r_mcangle_it 1.337 r_mcangle_other 1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.377 r_dihedral_angle_2_deg 8.691 r_dihedral_angle_1_deg 6.296 r_rigid_bond_restr 3.164 r_long_range_B_refined 2.124 r_long_range_B_other 2.054 r_angle_refined_deg 1.542 r_scangle_other 1.408 r_mcangle_it 1.337 r_mcangle_other 1.337 r_scbond_it 1.015 r_scbond_other 1.009 r_mcbond_it 0.919 r_mcbond_other 0.919 r_angle_other_deg 0.55 r_chiral_restr 0.088 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2961 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHENIX phasing