9H0Q | pdb_00009h0q

N terminal domain of BC2L-C lectin in complex with N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WQ4trimer
experimental modelPDB 6TIDmonomer

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29217% Peg10K, 100 mM sodium acetate and 100 mM Bis-Tris pH 5.5 cryo in 7.6% Peg10K, 22.5% Peg Smear Low, 45 mM sodium acetate and Bis Tris pH 5.5 and 3 mM PMA127
Crystal Properties
Matthews coefficientSolvent content
3.463.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.506α = 90
b = 169.506β = 90
c = 344.036γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2024-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.97856SOLEILPROXIMA 2

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
12.5548.9321000.0910.10.0410.99918.611.662109
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)
12.552.620.91610.4030.8312.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.5548.93262106306199.9690.1810.17910.18590.22190.226651.209
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]
0.8090.4040.809-2.623
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.526
r_dihedral_angle_2_deg15.217
r_dihedral_angle_6_deg14.188
r_lrange_it10.179
r_lrange_other10.17
r_scangle_it8.692
r_scangle_other8.691
r_dihedral_angle_1_deg7.343
r_mcangle_other7.209
r_mcangle_it7.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.526
r_dihedral_angle_2_deg15.217
r_dihedral_angle_6_deg14.188
r_lrange_it10.179
r_lrange_other10.17
r_scangle_it8.692
r_scangle_other8.691
r_dihedral_angle_1_deg7.343
r_mcangle_other7.209
r_mcangle_it7.208
r_scbond_it6.816
r_scbond_other6.816
r_mcbond_it5.635
r_mcbond_other5.625
r_angle_refined_deg1.889
r_angle_other_deg0.599
r_symmetry_xyhbond_nbd_refined0.286
r_symmetry_nbd_other0.215
r_nbd_refined0.199
r_nbtor_refined0.188
r_nbd_other0.165
r_xyhbond_nbd_refined0.15
r_symmetry_nbd_refined0.146
r_chiral_restr_other0.105
r_symmetry_nbtor_other0.093
r_chiral_restr0.087
r_ncsr_local_group_140.08
r_ncsr_local_group_410.077
r_ncsr_local_group_230.075
r_ncsr_local_group_260.075
r_ncsr_local_group_200.074
r_ncsr_local_group_380.074
r_ncsr_local_group_360.072
r_ncsr_local_group_130.071
r_ncsr_local_group_290.071
r_ncsr_local_group_420.071
r_ncsr_local_group_30.07
r_ncsr_local_group_100.07
r_ncsr_local_group_60.069
r_ncsr_local_group_110.069
r_ncsr_local_group_310.069
r_ncsr_local_group_430.068
r_ncsr_local_group_50.067
r_ncsr_local_group_210.067
r_ncsr_local_group_240.067
r_ncsr_local_group_270.067
r_ncsr_local_group_20.066
r_ncsr_local_group_340.066
r_ncsr_local_group_10.065
r_ncsr_local_group_120.065
r_ncsr_local_group_220.064
r_ncsr_local_group_280.063
r_ncsr_local_group_300.063
r_ncsr_local_group_80.062
r_ncsr_local_group_40.061
r_ncsr_local_group_180.061
r_ncsr_local_group_350.061
r_ncsr_local_group_150.06
r_ncsr_local_group_160.06
r_ncsr_local_group_370.059
r_ncsr_local_group_250.057
r_ncsr_local_group_320.057
r_ncsr_local_group_330.057
r_ncsr_local_group_390.057
r_ncsr_local_group_400.057
r_ncsr_local_group_450.057
r_ncsr_local_group_90.056
r_ncsr_local_group_190.056
r_ncsr_local_group_440.054
r_ncsr_local_group_70.052
r_ncsr_local_group_170.05
r_symmetry_xyhbond_nbd_other0.045
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9591
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms351

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing