8Q9Q | pdb_00008q9q

Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7 deacetylase binding motif


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8C84 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293200 mM sodium acetate trihydrate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v polyethylene glycol 3350 (PEG 3350)
Crystal Properties
Matthews coefficientSolvent content
1.9537

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.883α = 90
b = 59.361β = 90
c = 76.502γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2021-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.976ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1176.5960.0890.999118.814910
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)RedundancyNumber Unique Reflections (All)
12.112.1798.90.7320.8822.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1146.941417469296.060.266350.265320.270.284890.29RANDOM51.23
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]
-1.733.11-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.826
r_dihedral_angle_3_deg18.496
r_long_range_B_refined11.688
r_dihedral_angle_4_deg10.672
r_mcangle_it6.418
r_dihedral_angle_1_deg6.148
r_scbond_it5.642
r_mcbond_it4.595
r_angle_refined_deg1.705
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.826
r_dihedral_angle_3_deg18.496
r_long_range_B_refined11.688
r_dihedral_angle_4_deg10.672
r_mcangle_it6.418
r_dihedral_angle_1_deg6.148
r_scbond_it5.642
r_mcbond_it4.595
r_angle_refined_deg1.705
r_chiral_restr0.128
r_gen_planes_refined0.008
r_bond_refined_d0.006
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 AtomsNumber
Protein Atoms1642
Nucleic Acid Atoms574
Solvent Atoms46
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing