2XJT

X-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae in complex with calcium and Man5(D1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherUNPUBLISHED STRUCTURAL DATA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.5M NACL, 0.1 M BISTRIS-PROPANE PH7.5, 20% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7655.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.32α = 90
b = 62.01β = 90
c = 106.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-07-25MSINGLE 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
11.219.3997.40.0416.74.793590-310.4
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)
11.21.2699.90.334.74.6

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 DATA1.219.3391841171096.990.130860.130450.15316RANDOM11.664
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]
-0.170.17-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.129
r_dihedral_angle_3_deg12.497
r_dihedral_angle_4_deg8.097
r_dihedral_angle_1_deg6.327
r_scangle_it4.115
r_scbond_it2.953
r_mcangle_it2.347
r_angle_refined_deg1.616
r_mcbond_it1.488
r_rigid_bond_restr1.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.129
r_dihedral_angle_3_deg12.497
r_dihedral_angle_4_deg8.097
r_dihedral_angle_1_deg6.327
r_scangle_it4.115
r_scbond_it2.953
r_mcangle_it2.347
r_angle_refined_deg1.616
r_mcbond_it1.488
r_rigid_bond_restr1.184
r_angle_other_deg0.994
r_mcbond_other0.53
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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_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 Atoms422
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing