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X-ray structure of the adduct formed upon reaction of Lysozyme with K3[Ru2(CO3)4] in condition A
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, 0.6 M NaNO3, 0.1 M NaOAc pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.04 38.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.06 α = 90 b = 78.06 β = 90 c = 37.47 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 2022-07-15 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 1.18 55.2 99.2 0.034 1 42.5 22.2 38622
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 1.18 1.2 1.003 0.75 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 1.18 55.197 38106 1943 98.641 0.18 0.1788 0.1818 0.2016 0.2041 16.845
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] 0.023 0.023 -0.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.707 r_dihedral_angle_3_deg 14.4 r_dihedral_angle_2_deg 6.858 r_dihedral_angle_1_deg 6.472 r_lrange_it 5.701 r_lrange_other 5.38 r_scangle_it 4.138 r_scangle_other 4.027 r_scbond_it 2.809 r_scbond_other 2.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.707 r_dihedral_angle_3_deg 14.4 r_dihedral_angle_2_deg 6.858 r_dihedral_angle_1_deg 6.472 r_lrange_it 5.701 r_lrange_other 5.38 r_scangle_it 4.138 r_scangle_other 4.027 r_scbond_it 2.809 r_scbond_other 2.572 r_mcangle_other 2.196 r_mcangle_it 2.178 r_angle_refined_deg 1.827 r_mcbond_it 1.519 r_mcbond_other 1.518 r_angle_other_deg 0.606 r_nbd_refined 0.25 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.174 r_nbd_other 0.165 r_symmetry_nbd_refined 0.113 r_symmetry_xyhbond_nbd_refined 0.11 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing