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X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated triphenylphosphonium cation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 293 20% ethylene glycol
0.6 M sodium nitrate
0.1 M sodium acetate pH 4.4
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.443 α = 90 b = 78.443 β = 90 c = 37.385 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 2018-03-12 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 1.99 55.47 99.6 0.107 12.1 4.8 8433
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 1.99 2.02 99.5 0.569 0.827 1.7 4
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 1dpx 1.99 55.47 7994 413 99.73 0.17027 0.16651 0.1772 0.24184 0.2474 RANDOM 25.859
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] -0.19 -0.19 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.877 r_dihedral_angle_4_deg 21.535 r_dihedral_angle_3_deg 13.637 r_long_range_B_other 6.889 r_long_range_B_refined 6.888 r_dihedral_angle_1_deg 6.582 r_scangle_other 4.644 r_scbond_it 3.035 r_scbond_other 3.034 r_mcangle_it 2.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.877 r_dihedral_angle_4_deg 21.535 r_dihedral_angle_3_deg 13.637 r_long_range_B_other 6.889 r_long_range_B_refined 6.888 r_dihedral_angle_1_deg 6.582 r_scangle_other 4.644 r_scbond_it 3.035 r_scbond_other 3.034 r_mcangle_it 2.446 r_mcangle_other 2.446 r_angle_refined_deg 1.744 r_mcbond_it 1.693 r_mcbond_other 1.688 r_angle_other_deg 1.084 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 115 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing