2XJR

X-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae in complex with calcium and Man5(D2-D3)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherUNPUBLISHED STRUCTURAL DATA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.5 M NACL, 0.05 M BISTRIS-PROPANE PH 7.2, 20% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.7755.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.46α = 90
b = 61.91β = 90
c = 106.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-05-07MSINGLE 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
11.2519.4399.80.072110.785499-39.2
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)
11.251.3299.20.593.67.9

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 DATA1.2519.3583938156199.860.113690.113210.13996RANDOM10.392
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]
-0.70.090.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.889
r_dihedral_angle_3_deg11.511
r_dihedral_angle_4_deg9.709
r_dihedral_angle_1_deg6.098
r_scangle_it4.247
r_mcangle_it3.424
r_scbond_it3.072
r_mcbond_it2.383
r_angle_refined_deg2.06
r_angle_other_deg1.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.889
r_dihedral_angle_3_deg11.511
r_dihedral_angle_4_deg9.709
r_dihedral_angle_1_deg6.098
r_scangle_it4.247
r_mcangle_it3.424
r_scbond_it3.072
r_mcbond_it2.383
r_angle_refined_deg2.06
r_angle_other_deg1.449
r_mcbond_other1.223
r_rigid_bond_restr1.023
r_chiral_restr0.135
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_gen_planes_other0.003
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 Atoms1926
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing