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X-ray structure of the bis-platinum lysozyme adduct formed in the reaction between the protein and the two drugs Cisplatin and Oxaliplatin (preparation 2)
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 Best crystals grow within 2-10 days from the following conditions: 0.6 M NaNO3, 0.1 M sodium acetate pH 4.4 and 20 % ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 1.96 37.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.377 α = 90 b = 77.377 β = 90 c = 37.6 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+ 2014-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.95 54.71 95.8 0.113 11.7 5.7 8452
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 1.95 1.98 83.2 0.611 4.3
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 1.95 54.71 8023 403 95.85 0.16223 0.15877 0.17 0.22986 0.2458 RANDOM 27.601
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] -0.28 -0.28 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.534 r_dihedral_angle_4_deg 14.782 r_dihedral_angle_3_deg 12.279 r_long_range_B_refined 7.868 r_long_range_B_other 7.656 r_dihedral_angle_1_deg 6.208 r_scangle_other 5.093 r_angle_refined_deg 4.931 r_scbond_it 3.717 r_scbond_other 3.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.534 r_dihedral_angle_4_deg 14.782 r_dihedral_angle_3_deg 12.279 r_long_range_B_refined 7.868 r_long_range_B_other 7.656 r_dihedral_angle_1_deg 6.208 r_scangle_other 5.093 r_angle_refined_deg 4.931 r_scbond_it 3.717 r_scbond_other 3.715 r_mcangle_other 2.82 r_mcangle_it 2.815 r_mcbond_it 2.013 r_mcbond_other 1.981 r_angle_other_deg 1.42 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 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 136 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing