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Structure of PslG with an iminosugar inhibitor
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 64.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.604 α = 90 b = 97.604 β = 90 c = 119.852 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 2023-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.90137 Diamond I03
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 1.5 84.53 100 0.127 0.134 0.041 0.999 14.1 20.4 103277
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) 1.5 1.53 100 2.584 2.718 0.843 0.669 1.3 20.7
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 1.5 69.172 103156 5069 99.947 0.132 0.1306 0.1305 0.1596 0.1596 24.048
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] 0.418 0.209 0.418 -1.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.768 r_lrange_it 15.188 r_dihedral_angle_3_deg 10.952 r_scangle_it 10.324 r_scbond_it 7.745 r_dihedral_angle_2_deg 7.233 r_mcangle_it 6.757 r_dihedral_angle_1_deg 6.276 r_rigid_bond_restr 5.53 r_mcbond_it 5.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.768 r_lrange_it 15.188 r_dihedral_angle_3_deg 10.952 r_scangle_it 10.324 r_scbond_it 7.745 r_dihedral_angle_2_deg 7.233 r_mcangle_it 6.757 r_dihedral_angle_1_deg 6.276 r_rigid_bond_restr 5.53 r_mcbond_it 5.01 r_angle_refined_deg 1.827 r_nbtor_refined 0.318 r_nbd_refined 0.241 r_symmetry_xyhbond_nbd_refined 0.202 r_xyhbond_nbd_refined 0.166 r_symmetry_nbd_refined 0.161 r_chiral_restr 0.128 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3293 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing