1VK4

Crystal structure of PfkB Carbohydrate kinase (TM0415) from Thermotoga maritima at 1.91 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7277TRIS pH 7, 15% Ethanol , pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.0840.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.29α = 90
b = 68.53β = 90
c = 96.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-04-09MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.939244, 0.979414, 0.979121SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9119.7789.40.06627.312.62042027.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.912.02580.2099.48.11885

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.9119.7719333103889.40.170070.16760.21938RANDOM20.243
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]
0.27-0.720.45
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it8.508
r_dihedral_angle_1_deg6.17
r_scbond_it5.713
r_mcangle_it3.663
r_mcbond_it2.074
r_angle_refined_deg1.542
r_angle_other_deg0.873
r_symmetry_vdw_other0.31
r_nbd_other0.244
r_nbd_refined0.208
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it8.508
r_dihedral_angle_1_deg6.17
r_scbond_it5.713
r_mcangle_it3.663
r_mcbond_it2.074
r_angle_refined_deg1.542
r_angle_other_deg0.873
r_symmetry_vdw_other0.31
r_nbd_other0.244
r_nbd_refined0.208
r_symmetry_vdw_refined0.16
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.101
r_chiral_restr0.097
r_nbtor_other0.084
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2212
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
XDSdata scaling
SHELXmodel building
autoSHARPphasing
REFMACrefinement
CCP4data scaling
SHELXphasing