9GN6

Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in complex with the inhibitor SAHA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G0X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82932% (w/v) PEG 8000, 10% (v/v) glycerol and 0.5M KCl
Crystal Properties
Matthews coefficientSolvent content
3.1360.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.206α = 90
b = 146.206β = 90
c = 146.206γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16Mmirror2019-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.000000PETRA III, EMBL c/o DESYP13 (MX1)

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
11.9546.31000.020.0280.02116.31.937885-341.09
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9521000.8440.5970.5321.32

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.9546.27737871185999.9890.1390.13730.175648.525
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.891
r_dihedral_angle_3_deg13.017
r_dihedral_angle_2_deg9.305
r_lrange_it8.753
r_lrange_other8.639
r_dihedral_angle_1_deg6.455
r_scangle_it6.383
r_scangle_other6.382
r_scbond_it4.598
r_scbond_other4.596
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.891
r_dihedral_angle_3_deg13.017
r_dihedral_angle_2_deg9.305
r_lrange_it8.753
r_lrange_other8.639
r_dihedral_angle_1_deg6.455
r_scangle_it6.383
r_scangle_other6.382
r_scbond_it4.598
r_scbond_other4.596
r_mcangle_it4.457
r_mcangle_other4.456
r_mcbond_it3.392
r_mcbond_other3.39
r_angle_refined_deg1.962
r_angle_other_deg0.647
r_metal_ion_refined0.254
r_xyhbond_nbd_refined0.239
r_nbd_refined0.238
r_symmetry_nbd_other0.188
r_nbtor_refined0.185
r_nbd_other0.145
r_symmetry_nbd_refined0.12
r_symmetry_xyhbond_nbd_refined0.107
r_chiral_restr0.093
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.036
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2822
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing