4Z3E

Crystal structure of the lectin domain of PapG from E. coli BI47 in complex with SSEA4 in space group P212121


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J8S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.15M ZnAcetate, 0.05M ZnCl2, 0.1MTris pH 7.5, 13% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.0339.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.21α = 90
b = 52.22β = 90
c = 76.32γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00004SLSX06DA

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
11.843.199.90.08119.38.517523
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)
11.81.9199.50.683.512.8

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 REPLACEMENTTHROUGHOUT1j8s1.843.11752392399.910.18040.178070.22402RANDOM28.14
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]
-0.44-0.250.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.814
r_dihedral_angle_4_deg17.978
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg8.109
r_long_range_B_refined5.481
r_long_range_B_other5.083
r_scangle_other3.013
r_mcangle_it2.46
r_mcangle_other2.459
r_angle_refined_deg2.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.814
r_dihedral_angle_4_deg17.978
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg8.109
r_long_range_B_refined5.481
r_long_range_B_other5.083
r_scangle_other3.013
r_mcangle_it2.46
r_mcangle_other2.459
r_angle_refined_deg2.365
r_scbond_it1.937
r_scbond_other1.937
r_mcbond_it1.609
r_mcbond_other1.604
r_angle_other_deg1.124
r_chiral_restr0.132
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1667
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing