Crystal structure of carbohydrate transporter solute binding protein VEIS_2079 from Verminephrobacter eiseniae EF01-2, TARGET EFI-511009, a complex with D-TALITOL
Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal grow
pH: 7.5 Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-TALITOL) RESERVOIR: 0.2 M POTASSIUM SULFATE, 25% PEG3350 CRYOPROTECTION: RESERVOIR SOLUTION PLUS 25% (V/V) GLYCEROL VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 1.4→50 Å / Num. obs: 113208 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 33.9
Reflection shell
Resolution: 1.4→1.42 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.8 / % possible all: 95.4
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Processing
Software
Name
Version
Classification
SHELX
modelbuilding
ARP/wARP
modelbuilding
REFMAC
5.8.0073
refinement
HKL-3000
datareduction
HKL-3000
datascaling
SHELX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.569 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1509
3259
3 %
RANDOM
Rwork
0.12322
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obs
0.12403
106509
97.58 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK