6RGW

Photorhabdus asymbiotica lectin PHL in complex with O-methylated PGL-1-derived disaccharide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52934M NaCl, 100mM Hepes, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8657.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.893α = 90
b = 80.893β = 90
c = 113.642γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
11.7544.131000.0730.9991711.14400228.891
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)
11.751.841001.1280.7232.211.1

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 REPLACEMENTTHROUGHOUT5MXE1.7540.4841752220999.990.184790.183450.20972RANDOM29.377
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]
0.440.220.44-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.226
r_dihedral_angle_3_deg11.974
r_dihedral_angle_4_deg10.35
r_dihedral_angle_1_deg8.405
r_long_range_B_refined3.635
r_long_range_B_other3.475
r_scangle_other2.207
r_mcangle_it1.963
r_mcangle_other1.962
r_scbond_it1.516
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.226
r_dihedral_angle_3_deg11.974
r_dihedral_angle_4_deg10.35
r_dihedral_angle_1_deg8.405
r_long_range_B_refined3.635
r_long_range_B_other3.475
r_scangle_other2.207
r_mcangle_it1.963
r_mcangle_other1.962
r_scbond_it1.516
r_scbond_other1.516
r_mcbond_other1.299
r_mcbond_it1.298
r_angle_refined_deg1.27
r_angle_other_deg1.262
r_chiral_restr0.05
r_bond_refined_d0.005
r_gen_planes_refined0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2654
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms111

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing