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The X-ray structure of the adduct formed in the reaction between hen egg white lysozyme and compound 4, a platin(II) compound containing a O, S bidentate ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Crystals of hen egg white lysozyme (HEWL)-Pt compound adducts appeared in solutions consisting of 1.1 M NaCl, 0.1 M sodium acetate pH 4.4. Single crystals suitable for X-ray experiments were grown by the hanging drop vapor-diffusion method using a 1:1 ratio of reservoir solution and protein adducts solution with a protein concentration of about 15 mg / ml.
Crystal Properties Matthews coefficient Solvent content 1.98 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.983 α = 90 b = 77.983 β = 90 c = 37.281 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+ 2015-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 55.14 98.6 9.1 5.1 10170
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 1.85 1.88 90.4 5.1 2.8
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 4J1A 1.85 55.14 9669 478 98.7 0.17 0.167 0.1767 0.233 0.2362 RANDOM 24.18
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] 0.52 0.52 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.307 r_dihedral_angle_4_deg 20.655 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 6.574 r_long_range_B_refined 6.386 r_long_range_B_other 6.384 r_scangle_other 4.615 r_scbond_it 3.069 r_scbond_other 3.067 r_mcangle_other 2.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.307 r_dihedral_angle_4_deg 20.655 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 6.574 r_long_range_B_refined 6.386 r_long_range_B_other 6.384 r_scangle_other 4.615 r_scbond_it 3.069 r_scbond_other 3.067 r_mcangle_other 2.547 r_mcangle_it 2.543 r_mcbond_it 1.922 r_mcbond_other 1.896 r_angle_refined_deg 1.724 r_angle_other_deg 1.132 r_chiral_restr 0.135 r_bond_refined_d 0.019 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 130 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing