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X-ray structure of the adduct formed upon reaction of Lysozyme with K2[Ru2(DPhF)(CO3)3] in condition B
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 7.5 293 2.0 M sodium formate and 0.1 M HEPES buffer at pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.01 38.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.88 α = 90 b = 76.88 β = 90 c = 38.61 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 2022-06-13 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 1.07 54.36 99.8 0.038 1 36.3 19 51851
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 1.07 1.08 0.754 0.833 2.3
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 1.07 54.36 49863 2503 96.786 0.171 0.17 0.1796 0.1929 0.2007 12.596
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] -0.009 -0.009 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.177 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_2_deg 9.907 r_dihedral_angle_1_deg 6.84 r_lrange_it 6.451 r_lrange_other 5.47 r_scangle_other 3.286 r_scangle_it 3.072 r_angle_refined_deg 2.165 r_scbond_other 2.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.177 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_2_deg 9.907 r_dihedral_angle_1_deg 6.84 r_lrange_it 6.451 r_lrange_other 5.47 r_scangle_other 3.286 r_scangle_it 3.072 r_angle_refined_deg 2.165 r_scbond_other 2.124 r_scbond_it 2.023 r_mcangle_other 1.906 r_mcangle_it 1.888 r_mcbond_it 1.263 r_mcbond_other 1.24 r_angle_other_deg 0.737 r_xyhbond_nbd_refined 0.268 r_symmetry_nbd_refined 0.264 r_nbd_other 0.264 r_nbd_refined 0.253 r_symmetry_xyhbond_nbd_refined 0.231 r_symmetry_nbd_other 0.213 r_nbtor_refined 0.185 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.034 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing