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X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-FPhF)(O2CCH3)3] (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 4 293 20% ethylene glycol, 0.1 M sodium acetate buffer at pH 4.0, 0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 1.95 36.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.48 α = 90 b = 77.48 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 2022-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
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 1.38 54.79 99.9 0.047 0.99 21.8 10.3 23817
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 1.38 1.4 0.935 0.833 2.3
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 1.38 54.79 23817 1197 99.933 0.192 0.1901 0.197 0.2306 0.2402 24.069
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] -0.049 -0.049 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.303 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 16.08 r_dihedral_angle_1_deg 6.64 r_lrange_it 6.341 r_lrange_other 6.27 r_scangle_it 4.813 r_scangle_other 4.795 r_scbond_it 3.194 r_scbond_other 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.303 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 16.08 r_dihedral_angle_1_deg 6.64 r_lrange_it 6.341 r_lrange_other 6.27 r_scangle_it 4.813 r_scangle_other 4.795 r_scbond_it 3.194 r_scbond_other 3.14 r_mcangle_it 2.908 r_mcangle_other 2.908 r_mcbond_it 2.079 r_mcbond_other 2.075 r_angle_refined_deg 1.921 r_angle_other_deg 1.577 r_symmetry_xyhbond_nbd_refined 0.258 r_nbd_refined 0.234 r_nbd_other 0.227 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.198 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_other 0.154 r_metal_ion_refined 0.136 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 109 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing