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X-ray structure of the adduct formed upon reaction of the gold(I) N-heterocyclic carbene complex Au2 with lysozyme
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 7.5 293 2.0 M sodium formate
0.1 M hepes buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.93 36.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77 α = 90 b = 77 β = 90 c = 37.27 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 2021-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
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 1.1 34.43 95.6 0.059 0.062 0.013 0.999 28.4 17.9 44982
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 1.1 1.11 58.8 0.551 0.637 0.318 0.635 2.4 3.7
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 1.1 34.43 44409 2238 96.541 0.134 0.1322 0.1322 0.17 0.1701 16.618
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] 0.579 0.579 -1.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.254 r_dihedral_angle_other_3_deg 28.186 r_dihedral_angle_4_deg 21.801 r_rigid_bond_restr 17.524 r_dihedral_angle_1_deg 14.328 r_dihedral_angle_3_deg 13.987 r_mcbond_it 8.002 r_mcbond_other 7.953 r_scbond_it 7.591 r_scbond_other 7.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.254 r_dihedral_angle_other_3_deg 28.186 r_dihedral_angle_4_deg 21.801 r_rigid_bond_restr 17.524 r_dihedral_angle_1_deg 14.328 r_dihedral_angle_3_deg 13.987 r_mcbond_it 8.002 r_mcbond_other 7.953 r_scbond_it 7.591 r_scbond_other 7.585 r_lrange_it 7.478 r_lrange_other 7.467 r_scangle_it 6.983 r_scangle_other 6.979 r_mcangle_other 6.965 r_mcangle_it 6.938 r_angle_refined_deg 2.708 r_angle_other_deg 1.876 r_symmetry_xyhbond_nbd_refined 0.259 r_nbd_other 0.258 r_nbd_refined 0.245 r_symmetry_nbd_refined 0.243 r_xyhbond_nbd_refined 0.232 r_symmetry_nbd_other 0.217 r_nbtor_refined 0.188 r_chiral_restr 0.158 r_symmetry_xyhbond_nbd_other 0.111 r_symmetry_nbtor_other 0.105 r_bond_refined_d 0.037 r_gen_planes_refined 0.017 r_bond_other_d 0.009 r_metal_ion_refined 0.009 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing