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X-ray structure of the adduct formed upon reaction of the gold(I) N-heterocyclic carbene complex Au1 with RNase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 293 22% PEG4K
10 mM sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.18 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.72 α = 90 b = 32.72 β = 90.261 c = 72.71 γ = 90
Symmetry Space Group C 1 2 1
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 1.42 50.36 96.1 0.073 0.08 0.031 0.998 12.9 6.4 43467
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 1.42 1.45 94.2 0.599 0.661 0.248 0.807 3.6 6.7
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 1JVT 1.42 50.36 43467 96.068 0.191 0.1893 0.1972 0.219 0.2278 23.39
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] 0.019 0.084 -0.063 0.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.161 r_dihedral_angle_3_deg 13.492 r_dihedral_angle_4_deg 12.836 r_dihedral_angle_1_deg 7.061 r_lrange_it 6.924 r_lrange_other 6.852 r_scangle_it 4.526 r_scangle_other 4.504 r_mcangle_it 3.594 r_mcangle_other 3.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.161 r_dihedral_angle_3_deg 13.492 r_dihedral_angle_4_deg 12.836 r_dihedral_angle_1_deg 7.061 r_lrange_it 6.924 r_lrange_other 6.852 r_scangle_it 4.526 r_scangle_other 4.504 r_mcangle_it 3.594 r_mcangle_other 3.593 r_scbond_it 2.987 r_scbond_other 2.964 r_mcbond_it 2.338 r_mcbond_other 2.338 r_angle_refined_deg 1.791 r_angle_other_deg 1.544 r_symmetry_nbd_refined 0.221 r_nbd_other 0.219 r_nbd_refined 0.21 r_symmetry_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.186 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.165 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.013 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 1902 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing