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The X-ray structure of the adduct formed in the reaction between hen egg white lysozyme and complex I, a pentacoordinate Pt(II) compound containing 2,9-dimethyl-1,10-phenanthroline, dimethylfumarate, methyl and iodine as ligands
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 4.4 298 20% glycol ethylene
0.1 M sodium acetate pH 4.4
0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.361 α = 90 b = 78.361 β = 90 c = 37.353 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 CCD RIGAKU SATURN 944 2018-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.96 55.41 99.9 0.099 13.3 6.7 8815 23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.99 100 0.597 2.9 5
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 (Observed) 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 193L 1.96 27.05 8367 417 99.9 0.1698 0.16807 0.1778 0.20458 0.212 RANDOM 22.971
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] -0.06 -0.06 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.216 r_dihedral_angle_4_deg 22.698 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 6.877 r_long_range_B_other 5.892 r_long_range_B_refined 5.89 r_scangle_other 4.195 r_scbond_it 2.702 r_scbond_other 2.7 r_mcangle_it 2.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.216 r_dihedral_angle_4_deg 22.698 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 6.877 r_long_range_B_other 5.892 r_long_range_B_refined 5.89 r_scangle_other 4.195 r_scbond_it 2.702 r_scbond_other 2.7 r_mcangle_it 2.335 r_mcangle_other 2.335 r_mcbond_it 1.657 r_mcbond_other 1.619 r_angle_refined_deg 1.618 r_angle_other_deg 1.452 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing