2XJS

X-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae in complex with calcium and a1,2-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherUNPUBLISHED STRUCTURAL DATA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.5 M NACL, 100 MM BISTRIS-PROPANE PH 7.5, 20% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.7755.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.45α = 90
b = 61.96β = 90
c = 106.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.2419.4493.70.0420.53.685499-310.6
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)
11.241.372.40.442.93.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTUNPUBLISHED STRUCTURAL DATA1.319.4472600137496.860.123440.122920.15209RANDOM11.452
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]
0.080.25-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.22
r_dihedral_angle_3_deg11.326
r_dihedral_angle_4_deg6.515
r_dihedral_angle_1_deg5.825
r_scangle_it4.123
r_scbond_it2.924
r_angle_refined_deg2.2
r_mcangle_it2.161
r_angle_other_deg1.967
r_mcbond_it1.383
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.22
r_dihedral_angle_3_deg11.326
r_dihedral_angle_4_deg6.515
r_dihedral_angle_1_deg5.825
r_scangle_it4.123
r_scbond_it2.924
r_angle_refined_deg2.2
r_mcangle_it2.161
r_angle_other_deg1.967
r_mcbond_it1.383
r_rigid_bond_restr1.114
r_mcbond_other0.449
r_chiral_restr0.113
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1928
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing