2PU8

Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529822% PEG 2000MME, 0.3M sodium acetate, 0.1M TrisHCl, 8mM CHAPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5451.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 213.81α = 90
b = 83.24β = 90
c = 51.57γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic optics2005-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.1107.297.50.06714.47.254913535403
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)
12.12.15496.10.2766.27.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.165.685204450785271397.580.202730.202730.200140.25155RANDOM29.387
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]
-1.63-1.473.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.343
r_dihedral_angle_3_deg13.94
r_dihedral_angle_4_deg13.739
r_dihedral_angle_1_deg5.677
r_scangle_it2.22
r_scbond_it1.462
r_angle_refined_deg1.263
r_mcangle_it0.751
r_mcbond_it0.446
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.343
r_dihedral_angle_3_deg13.94
r_dihedral_angle_4_deg13.739
r_dihedral_angle_1_deg5.677
r_scangle_it2.22
r_scbond_it1.462
r_angle_refined_deg1.263
r_mcangle_it0.751
r_mcbond_it0.446
r_nbtor_refined0.301
r_symmetry_vdw_refined0.192
r_nbd_refined0.189
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.132
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5845
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
d*TREKdata reduction
CNSphasing