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X-ray structure of HEWL upon reaction with a Ruthenium(II)-arene Complexed with Glycosylated Carbene Ligands (5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 20% ethylene glycol, 0.1 M sodium acetate buffer at pH 4.0, 0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 1.98 37.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.43 α = 90 b = 77.43 β = 90 c = 37.9 γ = 90
Symmetry Space Group P 43 21 2
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 6M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 34.63 100 0.036 1 37.7 20 37300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.21 100 1.789 0.832 2.1 15
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 193L 1.2 34.63 35511 1804 97.006 0.181 0.1791 0.1864 0.2212 0.2293 19.694
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] 0.035 0.035 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.636 r_dihedral_angle_4_deg 21.725 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 6.343 r_lrange_it 5.873 r_lrange_other 5.603 r_scangle_it 3.783 r_scangle_other 3.646 r_scbond_it 2.643 r_scbond_other 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.636 r_dihedral_angle_4_deg 21.725 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 6.343 r_lrange_it 5.873 r_lrange_other 5.603 r_scangle_it 3.783 r_scangle_other 3.646 r_scbond_it 2.643 r_scbond_other 2.326 r_mcangle_other 2.257 r_mcangle_it 2.249 r_angle_refined_deg 1.845 r_angle_other_deg 1.589 r_mcbond_it 1.549 r_mcbond_other 1.527 r_symmetry_metal_ion_refined 0.687 r_nbd_other 0.264 r_nbd_refined 0.241 r_symmetry_nbd_refined 0.221 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.166 r_metal_ion_refined 0.105 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing