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The X-ray structure of the adduct formed in the reaction between hen egg white lysozyme and compound 3, 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 4.4 298 Crystals of hen egg white lysozyme-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 1.97 37.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.206 α = 90 b = 78.206 β = 90 c = 37.005 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 FR571 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 1.78 55.3 97.6 0.052 49.1 7.1 11254
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 1.78 1.81 81.4 0.231 3.8 3.8
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 1.78 55.3 10677 546 97.65 0.15542 0.15348 0.1667 0.19011 0.1981 RANDOM 21.269
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 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_4_deg 23.749 r_dihedral_angle_3_deg 12.559 r_long_range_B_other 7.048 r_long_range_B_refined 7.047 r_dihedral_angle_1_deg 6.797 r_scangle_other 5.109 r_scbond_it 3.412 r_scbond_other 3.309 r_mcangle_other 2.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_4_deg 23.749 r_dihedral_angle_3_deg 12.559 r_long_range_B_other 7.048 r_long_range_B_refined 7.047 r_dihedral_angle_1_deg 6.797 r_scangle_other 5.109 r_scbond_it 3.412 r_scbond_other 3.309 r_mcangle_other 2.394 r_mcangle_it 2.392 r_angle_refined_deg 1.99 r_mcbond_it 1.723 r_mcbond_other 1.723 r_angle_other_deg 1.198 r_chiral_restr 0.152 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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 149 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing