5ICN

HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BKX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.3563.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.815α = 90
b = 107.815β = 90
c = 134.161γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96862DiamondI24

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
13.393.493.10.382.52.413008
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)
13.33.56920.861.32.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4BKX3.393.41226369592.220.256940.254520.29949RANDOM34.069
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]
0.930.470.93-3.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.248
r_dihedral_angle_4_deg21.976
r_dihedral_angle_3_deg17.766
r_dihedral_angle_1_deg5.706
r_long_range_B_refined4.252
r_long_range_B_other4.252
r_mcangle_it2.456
r_mcangle_other2.456
r_scangle_other2.322
r_mcbond_other1.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.248
r_dihedral_angle_4_deg21.976
r_dihedral_angle_3_deg17.766
r_dihedral_angle_1_deg5.706
r_long_range_B_refined4.252
r_long_range_B_other4.252
r_mcangle_it2.456
r_mcangle_other2.456
r_scangle_other2.322
r_mcbond_other1.421
r_mcbond_it1.42
r_scbond_it1.311
r_scbond_other1.31
r_angle_refined_deg1.228
r_angle_other_deg0.76
r_chiral_restr0.061
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4365
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing