2DFU

Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WZOPDB ENTRY 1WZO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.4295sodium chloride, lithium sulfate, sodium citrate, pH 5.4, microbatch, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.3162.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.34α = 90
b = 73.412β = 111.78
c = 122.632γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2005-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.00SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.2301000.0830.07511.84.5787457874524.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.281000.3340.294.294.67869

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1WZO2.2307839278392395699.80.1980.1970.1970.224RANDOM41.2
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]
-1.364.455.54-4.18
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it3.12
c_mcangle_it2.13
c_scbond_it2.07
c_angle_deg1.4
c_mcbond_it1.32
c_improper_angle_d0.92
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it3.12
c_mcangle_it2.13
c_scbond_it2.07
c_angle_deg1.4
c_mcbond_it1.32
c_improper_angle_d0.92
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7795
Nucleic Acid Atoms
Solvent Atoms643
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing