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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.6 M sodium nitrate, 0.1 M sodium acetate pH 4.4, 20 %ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.95 36.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.318 α = 90 b = 77.318 β = 90 c = 37.325 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+ 2014-06-26 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 1.85 99 99.4 0.095 13.8 5.8 10100
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 92.2 0.471 3.1 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.85 54.67 9585 482 99.39 0.1584 0.15539 0.1661 0.21801 0.2158 RANDOM 26.816
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] -0.79 -0.79 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.407 r_dihedral_angle_4_deg 15.486 r_dihedral_angle_3_deg 11.386 r_long_range_B_refined 8.096 r_long_range_B_other 7.713 r_dihedral_angle_1_deg 6.302 r_scangle_other 5.213 r_scbond_it 3.822 r_scbond_other 3.814 r_mcangle_it 2.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.407 r_dihedral_angle_4_deg 15.486 r_dihedral_angle_3_deg 11.386 r_long_range_B_refined 8.096 r_long_range_B_other 7.713 r_dihedral_angle_1_deg 6.302 r_scangle_other 5.213 r_scbond_it 3.822 r_scbond_other 3.814 r_mcangle_it 2.991 r_mcangle_other 2.991 r_mcbond_it 2.226 r_mcbond_other 2.21 r_angle_refined_deg 1.842 r_angle_other_deg 0.989 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 129 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing