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X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-CNPhF)(O2CCH3)3]
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 at pH 4.0, and 0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.01 38.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.18 α = 90 b = 78.18 β = 90 c = 37.53 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 2022-07-16 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 1.13 55.28 86.94 0.042 1 21.8 9.9 38424
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 1.13 1.15 0.836 0.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.13 55.28 38424 1837 86.94 0.199 0.1982 0.205 0.2095 0.2155 RANDOM 20.479
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] -0.078 -0.078 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.243 r_dihedral_angle_6_deg 13.94 r_lrange_it 7.783 r_lrange_other 7.521 r_dihedral_angle_1_deg 6.278 r_dihedral_angle_2_deg 5.297 r_scangle_other 4.673 r_scangle_it 4.5 r_scbond_other 3.086 r_scbond_it 2.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.243 r_dihedral_angle_6_deg 13.94 r_lrange_it 7.783 r_lrange_other 7.521 r_dihedral_angle_1_deg 6.278 r_dihedral_angle_2_deg 5.297 r_scangle_other 4.673 r_scangle_it 4.5 r_scbond_other 3.086 r_scbond_it 2.986 r_mcangle_it 2.846 r_mcangle_other 2.844 r_angle_refined_deg 1.993 r_mcbond_it 1.969 r_mcbond_other 1.945 r_angle_other_deg 0.69 r_symmetry_nbd_refined 0.272 r_nbd_refined 0.25 r_symmetry_nbd_other 0.197 r_nbd_other 0.192 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.153 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.082 r_metal_ion_refined 0.069 r_bond_refined_d 0.012 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 127 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing