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X-ray structure of the adduct formed upon reaction of the gold compound AF-Npx with lysozyme (Structure 1)
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 7.5 298 .0 M sodium formate, 0.1 M Hepes buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.394 α = 90 b = 79.394 β = 90 c = 35.815 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 1.54 32.65 92.9 0.2 0.995 7.9 15.8 15114
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 1.54 1.64 42.9 3.965 0.633 1.4 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.54 32.65 15114 799 86.036 0.208 0.2058 0.2136 0.2505 0.2491 23.567
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] -0.075 -0.075 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_4_deg 20.136 r_dihedral_angle_3_deg 15.494 r_dihedral_angle_1_deg 6.691 r_lrange_it 6.165 r_lrange_other 6.077 r_scangle_it 4.15 r_scangle_other 4.147 r_mcangle_it 2.943 r_mcangle_other 2.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.686 r_dihedral_angle_4_deg 20.136 r_dihedral_angle_3_deg 15.494 r_dihedral_angle_1_deg 6.691 r_lrange_it 6.165 r_lrange_other 6.077 r_scangle_it 4.15 r_scangle_other 4.147 r_mcangle_it 2.943 r_mcangle_other 2.941 r_scbond_it 2.63 r_scbond_other 2.628 r_mcbond_it 1.974 r_mcbond_other 1.966 r_angle_refined_deg 1.63 r_angle_other_deg 1.443 r_xyhbond_nbd_refined 0.26 r_nbd_other 0.25 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.195 r_symmetry_nbd_refined 0.171 r_nbtor_refined 0.166 r_xyhbond_nbd_other 0.106 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 75 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing