4D3W

Crystal Structure of Epithelial Adhesin 1 A domain (Epa1A) from Candida glabrata in complex with the T-antigen (Galb1-3GalNAc)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ASLPDB ENTRY 4ASL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12915 MM CALCL2, 5 MM T-ANTIGEN (GAL-B-1, 3-GALNAC), 100 MM HEPES PH 7, 20% PEG 6000, 291 K
Crystal Properties
Matthews coefficientSolvent content
1.8132.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.01α = 90
b = 55.01β = 90
c = 139.75γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MARMOSAIC 255 MM2012-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.524.61000.113.410.935383-3
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)
11.51.581000.54.210.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4ASL1.524.6133528176799.930.159180.157940.18295RANDOM15.626
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]
-0.19-0.190.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.837
r_dihedral_angle_3_deg13.231
r_dihedral_angle_4_deg13.127
r_dihedral_angle_1_deg6.405
r_mcangle_it2.338
r_scbond_it1.615
r_angle_refined_deg1.611
r_mcbond_it1.377
r_mcbond_other1.361
r_angle_other_deg0.815
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.837
r_dihedral_angle_3_deg13.231
r_dihedral_angle_4_deg13.127
r_dihedral_angle_1_deg6.405
r_mcangle_it2.338
r_scbond_it1.615
r_angle_refined_deg1.611
r_mcbond_it1.377
r_mcbond_other1.361
r_angle_other_deg0.815
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_it
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 Atoms1807
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing