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Structure of the N terminal domain of Bc2L-C lectin (1-131) in complex with H-type 1 antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 1.2 M Na citrate pH 7.0
cryoprotected in 2.5 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 1.97 37.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.696 α = 90 b = 42.696 β = 90 c = 308.584 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2018-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.98096 ESRF BM30A
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.61 36.71 99.7 0.049 0.056 0.027 0.999 23.9 7.8 14606 18.4
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) Redundancy Number Unique Reflections (All) 1 1.61 1.64 97.5 0.588 0.643 0.32 0.874 3.7 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2wq4 1.614 36.71 14605 751 99.652 0.161 0.1583 0.1728 0.2027 0.2085 18.654
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] -0.186 -0.093 -0.186 0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.225 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_3_deg 11.052 r_dihedral_angle_1_deg 8.033 r_lrange_it 5.047 r_lrange_other 4.897 r_scangle_it 3.389 r_scangle_other 3.387 r_mcangle_it 2.526 r_mcangle_other 2.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.225 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_3_deg 11.052 r_dihedral_angle_1_deg 8.033 r_lrange_it 5.047 r_lrange_other 4.897 r_scangle_it 3.389 r_scangle_other 3.387 r_mcangle_it 2.526 r_mcangle_other 2.526 r_scbond_it 2.285 r_scbond_other 2.283 r_mcbond_it 1.789 r_mcbond_other 1.782 r_angle_refined_deg 1.779 r_angle_other_deg 1.555 r_nbd_refined 0.208 r_symmetry_nbd_other 0.196 r_symmetry_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.179 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.163 r_symmetry_nbd_refined 0.151 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 967 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing