4LHK

Structure of the N-terminal domain of the Lg-Flo1 adhesin (N-Lg-Flo1p) from the yeast Saccharomyces pastorianus, in complex with calcium and alpha-1,2-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XJQPDB ENTRY 2XJQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293Protein solution: 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 10 mM CaCl2 Crystallization condition: 0.1 M amino acids (L-Na-glutamate, DL-alanine, glycine, DL-lysine-HCl, DL-serine), 0.1 M imidazole-MES pH 6.5, 30% w/v PEG 550 MME - PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.618α = 90
b = 85.476β = 93.72
c = 68.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.98011SOLEILPROXIMA 1

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
11.7338.5497.30.0929.94.54485244852
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)
11.731.76960.7042.14.72430

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XJQ1.7335.134254842548227597.120.140230.140230.137410.19329RANDOM22.116
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]
0.19-0.050.07-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.426
r_sphericity_free31.222
r_sphericity_bonded13.206
r_dihedral_angle_3_deg12.252
r_dihedral_angle_4_deg10.724
r_dihedral_angle_1_deg6.812
r_rigid_bond_restr4.945
r_angle_refined_deg1.829
r_angle_other_deg1.13
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.426
r_sphericity_free31.222
r_sphericity_bonded13.206
r_dihedral_angle_3_deg12.252
r_dihedral_angle_4_deg10.724
r_dihedral_angle_1_deg6.812
r_rigid_bond_restr4.945
r_angle_refined_deg1.829
r_angle_other_deg1.13
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3372
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms48

Software

Software
Software NamePurpose
BALBESphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling