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X-ray structure of the adduct formed upon reaction of the gold compound AF-Npx with lysozyme (Structure 2)
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 6.5 298 14% PEG 8K, 0.1 M sodium citrate and 0.1 M sodium cacodylate buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.01 38.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.66 α = 90 b = 78.66 β = 90 c = 37.327 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 EIGER X 9M 2025-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9677 ESRF ID23-2
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 1.44 39.33 94.4 0.2 0.994 12.9 22.2 20064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.51 46.7 0.627 21.8 21.8
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 1.441 39.33 20047 935 92.2 0.181 0.1796 0.1883 0.1999 0.2032 20.467
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] -0.081 -0.081 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_4_deg 22.08 r_dihedral_angle_3_deg 15.447 r_lrange_it 7.388 r_lrange_other 7.321 r_dihedral_angle_1_deg 6.765 r_scangle_it 5.13 r_scangle_other 5.125 r_scbond_it 3.173 r_scbond_other 3.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_4_deg 22.08 r_dihedral_angle_3_deg 15.447 r_lrange_it 7.388 r_lrange_other 7.321 r_dihedral_angle_1_deg 6.765 r_scangle_it 5.13 r_scangle_other 5.125 r_scbond_it 3.173 r_scbond_other 3.173 r_mcangle_other 2.819 r_mcangle_it 2.804 r_mcbond_it 1.891 r_mcbond_other 1.855 r_angle_refined_deg 1.812 r_angle_other_deg 1.585 r_symmetry_nbd_refined 0.262 r_xyhbond_nbd_refined 0.235 r_nbd_refined 0.226 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.174 r_nbd_other 0.168 r_symmetry_xyhbond_nbd_refined 0.13 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.087 r_metal_ion_refined 0.024 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing