4LHN

Structure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) from the yeast Saccharomyces cerevisiae, in complex with calcium and mannose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293Protein solution: 50 mM sodium acetate pH 5, 150 mM NaCl, 10 mM CaCl2 Crystallization condition: 1 M NaCl, 15% v/v EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.7α = 90
b = 63.59β = 90
c = 106.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRIGAKU SATURN 944+2013-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12.1215.3790.10.112.35.71671816718
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)
12.122.2380.30.4333.75.62106

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 2XJQ2.1215.03158401584083989.560.148380.148380.146020.19405RANDOM26.134
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]
0.04-0.320.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.138
r_dihedral_angle_3_deg14.76
r_dihedral_angle_4_deg8.719
r_dihedral_angle_1_deg6.523
r_angle_refined_deg2.086
r_angle_other_deg0.898
r_chiral_restr0.114
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.138
r_dihedral_angle_3_deg14.76
r_dihedral_angle_4_deg8.719
r_dihedral_angle_1_deg6.523
r_angle_refined_deg2.086
r_angle_other_deg0.898
r_chiral_restr0.114
r_bond_refined_d0.02
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1901
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms13

Software

Software
Software NamePurpose
HKL-2000data collection
BALBESphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling