3GBU

Crystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in complex with ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EWMPDB entry 3EWM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529118% PEG 8000, 0.2M Calcium acetate, 0.1M Sodium cacodylate pH 6.5, ATP, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7354.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.148α = 90
b = 119.422β = 90
c = 178.81γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9792NSLSX29A

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
12.25097.83.27.1782037820329.1

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 3EWM2.249.667810778107394699.90.2160.2160.2160.242RANDOM37.2
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]
2.083.67-5.75
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.5
c_angle_deg1.3
c_improper_angle_d0.77
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9344
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms124

Software

Software
Software NamePurpose
CBASSdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling