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Structure of PslG with a covalently- bound pentasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6 277 20 mM MES pH 6.0, 50 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.44 64.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.692 α = 90 b = 97.692 β = 90 c = 119.775 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 EIGER2 XE 9M 2023-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.95392 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.55 84.604 100 0.155 0.057 0.999 11 16.2 93736
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.9 0.926 0.663 16.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.55 84.604 93683 4697 99.947 0.143 0.1419 0.1388 0.1739 0.1722 RANDOM 23.288
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] 0.361 0.181 0.361 -1.171
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.429 r_dihedral_angle_6_deg 15.041 r_dihedral_angle_3_deg 11.119 r_scangle_it 9.517 r_dihedral_angle_2_deg 7.766 r_scbond_it 7.084 r_dihedral_angle_1_deg 6.332 r_mcangle_it 6.077 r_rigid_bond_restr 5.225 r_mcbond_it 4.452
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.429 r_dihedral_angle_6_deg 15.041 r_dihedral_angle_3_deg 11.119 r_scangle_it 9.517 r_dihedral_angle_2_deg 7.766 r_scbond_it 7.084 r_dihedral_angle_1_deg 6.332 r_mcangle_it 6.077 r_rigid_bond_restr 5.225 r_mcbond_it 4.452 r_angle_refined_deg 1.738 r_nbtor_refined 0.319 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.19 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.126 r_bond_refined_d 0.013 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3309 Nucleic Acid Atoms Solvent Atoms 632 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing