4NGU

Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio alaskensis G20 (Dde_1548), Target EFI-510103, with bound D-Ala-D-Ala


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529836.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Ala-D-Ala, reservoir: 0.2 M sodium chloride, 0.1 M acetate, pH 4.5, 1.26 M ammonium sulfate, cryoprotection: 4:1 1.8 M lithium sulfate:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.7667.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.607α = 90
b = 91.607β = 90
c = 129.027γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEmirrors2013-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.574.6951000.1680.16813.315.6197021970234.76
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.641000.7640.764116.12819

Refinement

Statistics
Diffraction IDStructure Solution 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 DIFFRACTIONSAD2.540.9681951919519100099.350.19230.19230.18970.2421RANDOM15.8886
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.082
f_angle_d1.113
f_chiral_restr0.08
f_bond_d0.009
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2454
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms17

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing