2XJU | pdb_00002xju

X-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae with mutation S227A 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, BISTRIS-PROPANE PH7.5, 20% PEG-4000
Crystal Properties
Matthews coefficientSolvent content
2.7855.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.47α = 90
b = 62.57β = 90
c = 105.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOSMIC MIRRORS2009-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
11.6719.498.20.0518.43.535802-313.4
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)
11.671.7693.90.2753.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTUNPUBLISHED STRUCTURAL DATA1.719.43355862498.570.16450.16390.160.197110.2RANDOM15.914
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]
-0.210.7-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.717
r_dihedral_angle_3_deg12.455
r_dihedral_angle_4_deg8.704
r_dihedral_angle_1_deg5.418
r_scangle_it2.745
r_angle_refined_deg1.74
r_scbond_it1.715
r_mcangle_it1.222
r_mcbond_it0.688
r_chiral_restr0.1
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1936
Nucleic Acid Atoms
Solvent Atoms434
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing