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CML1 crystal structure in complex with Lewis a tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 1.6 M AMSO4, 100 mM trisodium pH 5.6. Crystal flashed freezed in liquid nitrogen after transfer in 2.5 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.925 α = 90 b = 73.925 β = 90 c = 119.592 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 PIXEL DECTRIS EIGER X 16M 2019-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 43.7 98.4 0.056 0.064 0.03 0.999 13 4.3 52412
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 1.95 2 99.4 0.5 0.575 0.274 0.851 4.2
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 6ZU2 1.95 43.7 52408 2590 98.328 0.189 0.1869 0.1713 0.2392 0.2219 31.1
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] -19.854 -19.854 39.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.644 r_dihedral_angle_4_deg 16.317 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_1_deg 7.427 r_lrange_it 5.69 r_lrange_other 5.625 r_scangle_it 5.424 r_scangle_other 5.235 r_scbond_it 4.328 r_scbond_other 4.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.644 r_dihedral_angle_4_deg 16.317 r_dihedral_angle_3_deg 12.002 r_dihedral_angle_1_deg 7.427 r_lrange_it 5.69 r_lrange_other 5.625 r_scangle_it 5.424 r_scangle_other 5.235 r_scbond_it 4.328 r_scbond_other 4.169 r_mcangle_other 4.055 r_mcangle_it 4.051 r_mcbond_it 3.546 r_mcbond_other 3.54 r_angle_refined_deg 1.734 r_angle_other_deg 1.46 r_symmetry_xyhbond_nbd_refined 0.197 r_nbd_other 0.196 r_nbd_refined 0.194 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_other 0.154 r_xyhbond_nbd_refined 0.15 r_xyhbond_nbd_other 0.121 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.088 r_ncsr_local_group_2 0.07 r_ncsr_local_group_6 0.068 r_ncsr_local_group_8 0.068 r_ncsr_local_group_7 0.066 r_ncsr_local_group_3 0.064 r_ncsr_local_group_9 0.063 r_ncsr_local_group_5 0.062 r_ncsr_local_group_15 0.062 r_ncsr_local_group_4 0.061 r_ncsr_local_group_12 0.061 r_ncsr_local_group_10 0.059 r_ncsr_local_group_11 0.059 r_ncsr_local_group_14 0.059 r_ncsr_local_group_13 0.056 r_ncsr_local_group_1 0.055 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5772 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 293
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing