9JWJ | pdb_00009jwj

Structure of Human HDAC2 in complex with inhibitor N-(2-amino-5-(furan-2-yl)phenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LY1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2910.1 M CHES pH 9.5, 35-38% (v/v) PEG 600
Crystal Properties
Matthews coefficientSolvent content
2.346.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.279α = 90
b = 98.562β = 90
c = 139.597γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U11SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.785091.20.0780.0880.0380.99710.84.9110377
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8891.80.6110.6790.2870.8054.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4LY11.7850104661559590.170.162070.159880.15930.202480.2013RANDOM30.272
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]
-0.891.63-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.622
r_dihedral_angle_4_deg23.896
r_dihedral_angle_3_deg14.091
r_long_range_B_refined8.168
r_dihedral_angle_1_deg5.851
r_scbond_it4.407
r_mcangle_it3.513
r_mcbond_it2.617
r_angle_refined_deg1.951
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.622
r_dihedral_angle_4_deg23.896
r_dihedral_angle_3_deg14.091
r_long_range_B_refined8.168
r_dihedral_angle_1_deg5.851
r_scbond_it4.407
r_mcangle_it3.513
r_mcbond_it2.617
r_angle_refined_deg1.951
r_chiral_restr0.161
r_bond_refined_d0.02
r_gen_planes_refined0.012
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 Atoms8884
Nucleic Acid Atoms
Solvent Atoms734
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing