4A3X

Structure of the N-terminal domain of the Epa1 adhesin (Epa1-Np) from the pathogenic yeast Candida glabrata, in complex with calcium and lactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XJPPDB ENTRY 2XJP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.450 MM TRIS-HCL, 200 MM NACL, 10 MM CACL2, 20 MM LACTOSE, 100 MM HEPES PH 7.5, 22.5% PEG8000.
Crystal Properties
Matthews coefficientSolvent content
2.3354.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.481α = 90
b = 105.453β = 90
c = 69.571γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DASLSX06DA

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
11.654299.10.06206.93362522.5
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)
11.651.6987.70.463.25.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XJP1.6542.023192916811000.173580.17170.20969RANDOM15.666
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]
-0.550.63-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.514
r_dihedral_angle_4_deg11.532
r_dihedral_angle_3_deg11.418
r_dihedral_angle_1_deg7.089
r_scangle_it4.787
r_scbond_it3.358
r_mcangle_it2.362
r_angle_refined_deg2.226
r_mcbond_it1.438
r_chiral_restr0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.514
r_dihedral_angle_4_deg11.532
r_dihedral_angle_3_deg11.418
r_dihedral_angle_1_deg7.089
r_scangle_it4.787
r_scbond_it3.358
r_mcangle_it2.362
r_angle_refined_deg2.226
r_mcbond_it1.438
r_chiral_restr0.199
r_bond_refined_d0.032
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
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 Atoms1788
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing