7R55

B-trefoil lectin from Salpingoeca rosetta in complex with Gb3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7QE4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52920.1 M MOPSO, Bis-Tris pH 6.5, 100 mM amino acids Morpheus I, 35 % PEG SMEAR MEDIUM
Crystal Properties
Matthews coefficientSolvent content
2.40348.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.341α = 90
b = 58.997β = 90
c = 210.306γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978565SOLEILPROXIMA 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
11.8445.1899.80.0930.1060.050.99911.88.262904
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)
11.841.881.0341.1850.5720.7927.8

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-VALUE7QE41.8445.1862818298299.7550.1870.18440.239627.838
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]
2.658-1.087-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.779
r_dihedral_angle_4_deg16.464
r_dihedral_angle_3_deg13.207
r_dihedral_angle_1_deg7.599
r_lrange_it6.748
r_lrange_other6.673
r_scangle_it5.544
r_scangle_other5.544
r_scbond_it4.148
r_scbond_other4.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.779
r_dihedral_angle_4_deg16.464
r_dihedral_angle_3_deg13.207
r_dihedral_angle_1_deg7.599
r_lrange_it6.748
r_lrange_other6.673
r_scangle_it5.544
r_scangle_other5.544
r_scbond_it4.148
r_scbond_other4.148
r_mcangle_it4.089
r_mcangle_other4.089
r_mcbond_it3.214
r_mcbond_other3.214
r_angle_refined_deg2.103
r_angle_other_deg1.487
r_nbd_other0.231
r_symmetry_xyhbond_nbd_other0.223
r_symmetry_nbd_refined0.212
r_nbd_refined0.199
r_symmetry_nbd_other0.189
r_symmetry_xyhbond_nbd_refined0.178
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.171
r_ncsr_local_group_10.129
r_chiral_restr0.102
r_symmetry_nbtor_other0.086
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4956
Nucleic Acid Atoms
Solvent Atoms604
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building
XDSdata reduction