3TY5

Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72950.2-0.25 M di-ammoinium tartrate and 20% (w/v) Polyethylene Glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3948.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.989α = 90
b = 94.381β = 93.51
c = 75.314γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130PIXELDECTRIS PILATUS 6MSee Beamline Documentation2011-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
12.45099.130993-3

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD2.444.331.3733879172896.70.180.17760.2247Random
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]
4.10587.70620.7172-4.823
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.13
f_angle_d1.102
f_chiral_restr0.06
f_bond_d0.006
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6100
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms68

Software

Software
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing