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Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7 deacetylase binding motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM sodium acetate trihydrate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v polyethylene glycol 3350 (PEG 3350)
Crystal Properties Matthews coefficient Solvent content 1.95 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.883 α = 90 b = 59.361 β = 90 c = 76.502 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 9M 2021-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.11 76.5 96 0.089 0.999 11 8.8 14910
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.17 98.9 0.732 0.882 2.5
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 2.11 46.94 14174 692 96.06 0.26635 0.26532 0.2701 0.28489 0.2899 RANDOM 51.23
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] -1.73 3.11 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_3_deg 18.496 r_long_range_B_refined 11.688 r_dihedral_angle_4_deg 10.672 r_mcangle_it 6.418 r_dihedral_angle_1_deg 6.148 r_scbond_it 5.642 r_mcbond_it 4.595 r_angle_refined_deg 1.705 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_3_deg 18.496 r_long_range_B_refined 11.688 r_dihedral_angle_4_deg 10.672 r_mcangle_it 6.418 r_dihedral_angle_1_deg 6.148 r_scbond_it 5.642 r_mcbond_it 4.595 r_angle_refined_deg 1.705 r_chiral_restr 0.128 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 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 1642 Nucleic Acid Atoms 574 Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing