2VCG

Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZZ0PDB ENTRY 1ZZ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5600 MM NACL 200 MM NA-CACODYLATE 6.5
Crystal Properties
Matthews coefficientSolvent content
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.664α = 90
b = 93.633β = 103.99
c = 121.664γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.950960.0816.92.91116302
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)
11.91.9793.80.364.22.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ZZ01.9117.851060115596960.1590.1560.160.2060.21RANDOM16.34
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]
0.46-0.29-0.620.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.91
r_dihedral_angle_4_deg18.05
r_dihedral_angle_3_deg12.677
r_dihedral_angle_1_deg6.223
r_scangle_it2.881
r_scbond_it1.836
r_angle_refined_deg1.345
r_mcangle_it1.103
r_mcbond_it0.626
r_nbtor_refined0.31
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11099
Nucleic Acid Atoms
Solvent Atoms1694
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing