1ZZ1

Crystal structure of a HDAC-like protein with SAHA bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293NaCl, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.606α = 90
b = 94.716β = 104.75
c = 123.924γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97848ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5750
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.6351.1

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 DIFFRACTIONSADTHROUGHOUT1.5738.38171414906984.590.173660.172190.20132RANDOM16.498
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_2_deg36.726
r_dihedral_angle_4_deg16.224
r_dihedral_angle_3_deg12.406
r_dihedral_angle_1_deg6.227
r_scangle_it3.059
r_scbond_it2.055
r_angle_refined_deg1.456
r_mcangle_it1.15
r_mcbond_it0.708
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.726
r_dihedral_angle_4_deg16.224
r_dihedral_angle_3_deg12.406
r_dihedral_angle_1_deg6.227
r_scangle_it3.059
r_scbond_it2.055
r_angle_refined_deg1.456
r_mcangle_it1.15
r_mcbond_it0.708
r_nbtor_refined0.31
r_metal_ion_refined0.238
r_nbd_refined0.226
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.126
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10988
Nucleic Acid Atoms
Solvent Atoms1450
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing