2Z09

Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WJG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629310mM AMP-PCP, 100mM Magnesium Chloride, 0.09M Sodium acetate trihydrate, 1.8M Sodium chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8934.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.22α = 90
b = 75.9β = 90
c = 88.66γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102006-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0000SPring-8BL26B2

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
11.652095.30.04830.96.51326313.5
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)
1.651.671000.27.825.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1WJG1.6519.2213222135994.90.210.210.249RANDOM15.4
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]
2.650.12-2.78
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.1
c_scangle_it3.56
c_scbond_it2.43
c_angle_deg2.4
c_mcangle_it2.08
c_improper_angle_d1.65
c_mcbond_it1.4
c_bond_d0.029
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.1
c_scangle_it3.56
c_scbond_it2.43
c_angle_deg2.4
c_mcangle_it2.08
c_improper_angle_d1.65
c_mcbond_it1.4
c_bond_d0.029
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 Atoms916
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms33

Software

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