5MXG

Photorhabdus asymbiotica lectin (PHL) in complex with blood group H trisaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MXE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52903.7-4.3 M NaCl, 100 mM Hepes pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6252.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.309α = 90
b = 80.309β = 90
c = 112.973γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.895BESSY14.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.243.851000.0850.99923.812.421984
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.32980.7420.8853.812.5

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 REPLACEMENTTHROUGHOUT5MXE2.243.8520916103599.980.187320.185290.22842RANDOM40.284
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]
0.580.290.58-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.96
r_dihedral_angle_3_deg12.026
r_dihedral_angle_4_deg8.259
r_dihedral_angle_1_deg7.479
r_long_range_B_refined5.262
r_long_range_B_other5.261
r_scangle_other3.952
r_mcangle_it3.569
r_mcangle_other3.567
r_scbond_it2.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.96
r_dihedral_angle_3_deg12.026
r_dihedral_angle_4_deg8.259
r_dihedral_angle_1_deg7.479
r_long_range_B_refined5.262
r_long_range_B_other5.261
r_scangle_other3.952
r_mcangle_it3.569
r_mcangle_other3.567
r_scbond_it2.653
r_scbond_other2.652
r_mcbond_it2.47
r_mcbond_other2.47
r_angle_refined_deg1.511
r_angle_other_deg0.971
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms2658
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing