6LI7

Crystal Structure of Lectin from Pleurotus ostreatus in complex with GalNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W5N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.53000.9M Na2HPO4/K2HPO4, pH 5.5, 33% glycerol
Crystal Properties
Matthews coefficientSolvent content
6.2680.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.273α = 90
b = 152.273β = 90
c = 145.975γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16MSi 111. Rosenbaum-Rock double-crystal monochromator2018-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.99APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0983099.90.99616.3558637
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.180.996

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3W5N2.09829.64258628200099.8990.1930.19270.205532.103
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]
0.0060.0030.006-0.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.148
r_dihedral_angle_4_deg22.108
r_dihedral_angle_3_deg12.688
r_dihedral_angle_1_deg10.495
r_lrange_it7.483
r_lrange_other7.307
r_scangle_it6.244
r_scangle_other6.242
r_scbond_it4.601
r_scbond_other4.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.148
r_dihedral_angle_4_deg22.108
r_dihedral_angle_3_deg12.688
r_dihedral_angle_1_deg10.495
r_lrange_it7.483
r_lrange_other7.307
r_scangle_it6.244
r_scangle_other6.242
r_scbond_it4.601
r_scbond_other4.6
r_mcangle_it3.861
r_mcangle_other3.86
r_mcbond_it2.922
r_mcbond_other2.921
r_angle_refined_deg2.098
r_angle_other_deg1.469
r_nbd_refined0.21
r_xyhbond_nbd_refined0.207
r_symmetry_nbd_other0.198
r_symmetry_xyhbond_nbd_refined0.18
r_nbtor_refined0.177
r_nbd_other0.144
r_symmetry_xyhbond_nbd_other0.101
r_metal_ion_refined0.1
r_symmetry_nbtor_other0.098
r_chiral_restr0.089
r_symmetry_nbd_refined0.069
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2505
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
BALBESphasing