X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5292.1520% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound for co-crystallisation
Crystal Properties
Matthews coefficientSolvent content
1.9236.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.222α = 90
b = 76.066β = 90
c = 107.148γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9786SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.8448.2299.90.0680.0710.0190.99923.913.435137
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.8897.90.4690.4880.1330.94313.1

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 REPLACEMENTTHROUGHOUT1OKO1.8444.0133319177699.820.19450.19290.2255RANDOM21.196
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]
-0.430.71-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.501
r_dihedral_angle_4_deg20.038
r_dihedral_angle_3_deg10.736
r_dihedral_angle_1_deg7.037
r_angle_refined_deg1.545
r_angle_other_deg1.459
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.501
r_dihedral_angle_4_deg20.038
r_dihedral_angle_3_deg10.736
r_dihedral_angle_1_deg7.037
r_angle_refined_deg1.545
r_angle_other_deg1.459
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3578
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms58

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing