3MU6

Inhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by Small Molecules


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EGWPDB ENTRY 1EGW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop4.729150 mM acetic acid, 142mM NaCl, 5mM MgCl2, 10mM CaCl2, 3.3% Glycerol, 22.5% 3K PEG, pH 4.7, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6453.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.567α = 114.12
b = 61.622β = 89.99
c = 61.478γ = 89.95
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.435095.60.06718.52.419854
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.432.5293.90.2552.31954

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1EGW2.43433.444219819102694.760.2310.230.25132.949
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]
-5.58-0.4590.8377.447-11.446-1.867
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d23.841
f_angle_d1.33
f_chiral_restr0.068
f_bond_d0.008
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2344
Nucleic Acid Atoms1382
Solvent Atoms
Heterogen Atoms25

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction