5IWG

HDAC2 WITH LIGAND BRD4884


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293PEG 400, potassium phosphate
Crystal Properties
Matthews coefficientSolvent content
2.5451.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.297α = 90
b = 98.013β = 90
c = 139.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MKB mirror pair2013-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

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
11.6680.1595.20.0639.422.5141832
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)
11.661.9197.30.332.912.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6648.35138529330395.230.185560.185020.20778RANDOM23.947
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]
-0.340.75-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.786
r_dihedral_angle_4_deg18.303
r_dihedral_angle_3_deg10.779
r_dihedral_angle_1_deg6.215
r_long_range_B_refined5.758
r_long_range_B_other5.539
r_scangle_other1.697
r_angle_refined_deg1.409
r_angle_other_deg1.196
r_scbond_it1.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.786
r_dihedral_angle_4_deg18.303
r_dihedral_angle_3_deg10.779
r_dihedral_angle_1_deg6.215
r_long_range_B_refined5.758
r_long_range_B_other5.539
r_scangle_other1.697
r_angle_refined_deg1.409
r_angle_other_deg1.196
r_scbond_it1.077
r_scbond_other1.075
r_mcangle_other0.966
r_mcangle_it0.965
r_mcbond_it0.58
r_mcbond_other0.579
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms8866
Nucleic Acid Atoms
Solvent Atoms697
Heterogen Atoms158

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing