6T9A

Crystal structrue of RSL W31FW76F lectin mutant in complex with L-fucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BT9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.229323% PEG 6000, 0.1M Glycine, 0.1M Tris/HCl, pH 8.2
Crystal Properties
Matthews coefficientSolvent content
1.935.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.262α = 116.4
b = 42.105β = 94.54
c = 44.02γ = 115.49
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-10-12MSINGLE 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)R Sym 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
1237.1596.40.0530.0530.0710.0480.9948.321431514315
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1195.30.160.0470.0630.0410.9332

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 REPLACEMENTTHROUGHOUT2BT9237.151351778996.310.15470.15220.1982RANDOM23.392
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]
-0.77-1.32-0.940.640.830.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.801
r_dihedral_angle_3_deg10.375
r_dihedral_angle_1_deg7.459
r_dihedral_angle_4_deg5.174
r_angle_refined_deg1.309
r_angle_other_deg1.137
r_chiral_restr0.038
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.801
r_dihedral_angle_3_deg10.375
r_dihedral_angle_1_deg7.459
r_dihedral_angle_4_deg5.174
r_angle_refined_deg1.309
r_angle_other_deg1.137
r_chiral_restr0.038
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1977
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms133

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing