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Structure of FAB-fragment GB11 in complex with Sialyl Lewis A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XTG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 sodium malonate PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.51 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.838 α = 89.602 b = 108.697 β = 87.339 c = 108.92 γ = 89.251
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2021-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 26.98 98.2 0.407 0.222 0.915 2.8 3 40947 49.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.02 2.583 1.359 0.189 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.96 26.696 37583 1994 98.697 0.212 0.2097 0.2166 0.2479 0.2552 61.588
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] 2.256 -1.535 0.416 0.204 0.366 -2.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.574 r_lrange_it 13.77 r_lrange_other 13.77 r_dihedral_angle_6_deg 12.744 r_mcangle_it 8.594 r_mcangle_other 8.594 r_scangle_it 8.284 r_scangle_other 8.284 r_dihedral_angle_1_deg 7.814 r_dihedral_angle_2_deg 6.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.574 r_lrange_it 13.77 r_lrange_other 13.77 r_dihedral_angle_6_deg 12.744 r_mcangle_it 8.594 r_mcangle_other 8.594 r_scangle_it 8.284 r_scangle_other 8.284 r_dihedral_angle_1_deg 7.814 r_dihedral_angle_2_deg 6.989 r_mcbond_it 5.303 r_mcbond_other 5.302 r_scbond_it 5.015 r_scbond_other 5.015 r_angle_refined_deg 1.321 r_angle_other_deg 0.741 r_symmetry_xyhbond_nbd_refined 0.341 r_nbd_other 0.271 r_xyhbond_nbd_refined 0.259 r_nbd_refined 0.252 r_symmetry_nbd_other 0.232 r_symmetry_nbd_refined 0.212 r_nbtor_refined 0.179 r_ncsr_local_group_3 0.15 r_ncsr_local_group_11 0.148 r_ncsr_local_group_12 0.148 r_xyhbond_nbd_other 0.132 r_ncsr_local_group_2 0.099 r_ncsr_local_group_1 0.098 r_ncsr_local_group_9 0.096 r_ncsr_local_group_8 0.091 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_5 0.088 r_ncsr_local_group_7 0.088 r_ncsr_local_group_10 0.088 r_ncsr_local_group_4 0.085 r_ncsr_local_group_6 0.083 r_symmetry_xyhbond_nbd_other 0.075 r_chiral_restr 0.06 r_ext_dist_refined_b 0.01 r_gen_planes_other 0.006 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13216 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing