1V1A

2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V19 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5298VAPOUR-DIFFUSION SITTING DROP AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM KDG AND 5 MM AMP-PNP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH 8.5. BEFORE THE DATA COLLECTION THE CRYSTAL WAS SOAKED IN SOLUTION CONTAINING 0.35 M MAGNESIUM CHLORIDE INSTEAD OF AMMONIUM SULFATE. THE CRYOPROTECTANT CONTAINED 33% OF ETHYLENE GLYCOL IN ADDITION TO MAGNESIUM CHLORIDE, BUFFER AND LIGANDS
Crystal Properties
Matthews coefficientSolvent content
2.5352.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.321α = 90
b = 84.321β = 90
c = 168.701γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE R-AXISV2003-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B1SPring-8BL26B1

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
12.13097.90.05619.64.5838730-0.413.1
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)
12.12.1896.20.3552.68

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 REPLACEMENTTHROUGHOUTPDB ENTRY V192.129.8237822185295.70.17980.17980.2677RANDOM51.4
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]
-3.709-3.064-3.7097.417
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_scangle_it11.51
c_scbond_it8.64
c_mcangle_it8.46
c_mcbond_it5.94
c_angle_deg1.3
c_improper_angle_d0.85
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_scangle_it11.51
c_scbond_it8.64
c_mcangle_it8.46
c_mcbond_it5.94
c_angle_deg1.3
c_improper_angle_d0.85
c_bond_d0.008
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 Atoms4594
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms78

Software

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