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X-ray structure of the gold/lysozyme adduct formed upon 24h exposure of protein crystals to compound 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 4.5 293 20% ethylene glycol
0.1 M sodium acetate pH 4.5
0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.328 α = 90 b = 78.328 β = 90 c = 37.691 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 CCD RIGAKU SATURN 944 2019-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.12 55.39 98.3 0.132 0.06 0.752 10.4 5.3 6962
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.16 90.5 0.645 0.358 0.927 1.6 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 193L 2.12 33.99 6574 359 98.23 0.2149 0.2108 0.2174 0.2945 0.2979 RANDOM 24.733
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] -0.18 -0.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.217 r_dihedral_angle_4_deg 17.589 r_dihedral_angle_3_deg 15.606 r_dihedral_angle_1_deg 6.874 r_angle_refined_deg 1.556 r_angle_other_deg 1.283 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.217 r_dihedral_angle_4_deg 17.589 r_dihedral_angle_3_deg 15.606 r_dihedral_angle_1_deg 6.874 r_angle_refined_deg 1.556 r_angle_other_deg 1.283 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing