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The X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) terpyridine compound (pH 7.0)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.8 M succinic acid/NaOH, 0.10 M HEPES pH 7.0, 1% MPEG 2K
Crystal Properties Matthews coefficient Solvent content 2.01 38.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.455 α = 90 b = 79.455 β = 90 c = 36.49 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 2016-03-16 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) Rpim I (All) CC (Half) 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 1.96 56.18 99.3 0.084 0.04 0.812 8.1 2.8 8823
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.99 100 0.478 0.256 3.1 2.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1.96 56.18 8356 435 99.25 0.19093 0.18762 0.1962 0.24993 0.2534 RANDOM 34.567
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] -0.23 -0.23 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 19.234 r_dihedral_angle_3_deg 13.281 r_long_range_B_refined 7.635 r_long_range_B_other 7.562 r_dihedral_angle_1_deg 6.798 r_scangle_other 6.262 r_scbond_it 3.812 r_scbond_other 3.808 r_mcangle_other 3.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 19.234 r_dihedral_angle_3_deg 13.281 r_long_range_B_refined 7.635 r_long_range_B_other 7.562 r_dihedral_angle_1_deg 6.798 r_scangle_other 6.262 r_scbond_it 3.812 r_scbond_other 3.808 r_mcangle_other 3.379 r_mcangle_it 3.378 r_mcbond_it 2.619 r_mcbond_other 2.597 r_angle_refined_deg 1.817 r_angle_other_deg 1.119 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 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 104 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing