6RFZ

Photorhabdus laumondii lectin PLL2 in complex with D-glucose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62938% PEG 4000, 150 mM sodium acetate pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.6453.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.498α = 90
b = 71.099β = 103.95
c = 86.221γ = 90
Symmetry
Space GroupI 1 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
11.847.39990.2880.9033.43.83526213.025
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)
11.81.998.81.0450.4521.53.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.845.6433419167298.370.211560.210370.23497RANDOM15.456
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]
0.311.05-0.81-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.45
r_dihedral_angle_3_deg12.008
r_dihedral_angle_1_deg7.746
r_dihedral_angle_4_deg7.093
r_long_range_B_refined3.403
r_long_range_B_other3.052
r_angle_other_deg2.388
r_angle_refined_deg1.192
r_mcangle_it0.652
r_mcangle_other0.652
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.45
r_dihedral_angle_3_deg12.008
r_dihedral_angle_1_deg7.746
r_dihedral_angle_4_deg7.093
r_long_range_B_refined3.403
r_long_range_B_other3.052
r_angle_other_deg2.388
r_angle_refined_deg1.192
r_mcangle_it0.652
r_mcangle_other0.652
r_scangle_other0.606
r_mcbond_it0.385
r_mcbond_other0.383
r_scbond_it0.369
r_scbond_other0.369
r_chiral_restr0.042
r_bond_other_d0.037
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_refined_d0.003
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 Atoms2616
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing