4LN5

Crystal structure of a trap periplasmic solute binding protein from burkholderia ambifaria (Bamb_6123), TARGET EFI-510059, with bound glycerol and chloride ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PFY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5298Protein (16.23 mg/ml, 10 mM HEPES pH 7.5, 150mM NaCl, 5% glycerol, 5 mM DTT), Reservoir (0.8 M Lithium Chloride, 0.1 M Tris pH 8.5, 32%(w/v) PEG 4000 (MCSG1 C9)), Cryoprotection (20% Reservoir, 80% of 50% PEG3350), sitting drop vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.098α = 90
b = 97.34β = 90
c = 58.115γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2013-07-02MSINGLE 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
12.168.3861000.1360.13611.37.21628916289
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)
12.12.211000.6680.6681.26.82341

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENT2PFY2.148.67162691626982099.860.15740.15740.15420.2199RANDOM25.7937
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_d13.637
f_angle_d1.031
f_chiral_restr0.07
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2336
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms8

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
BALBESphasing