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Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 72 h of soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293 Crystals of beta-Lactoglobulin were grown using 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer pH 6.9 as reservoir. Protein crystallizes at a concentration of 18 mg/mL. Crystals of beta-Lactoglobulin were soaked in a solution consisting of 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer (pH 6.9) with 5 mM CDDP (about 1:3 protein to metal ratio).
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.62 α = 70.27 b = 48.8 β = 68.49 c = 49.18 γ = 76.99
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 2020-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2 43.91 86 0.077 0.996 10.2 3.4 17566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.06 83.7 0.235 0.89 3.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BEB 2.005 23.295 15643 782 76.633 0.203 0.1984 0.2015 0.2834 0.2853 22.458
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] -0.244 -0.094 0.692 0.809 1.641 0.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_3_deg 16.986 r_dihedral_angle_4_deg 15.134 r_dihedral_angle_1_deg 7.776 r_lrange_it 6.764 r_lrange_other 6.74 r_scangle_it 3.388 r_scangle_other 3.332 r_mcangle_it 3.286 r_mcangle_other 3.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_3_deg 16.986 r_dihedral_angle_4_deg 15.134 r_dihedral_angle_1_deg 7.776 r_lrange_it 6.764 r_lrange_other 6.74 r_scangle_it 3.388 r_scangle_other 3.332 r_mcangle_it 3.286 r_mcangle_other 3.285 r_scbond_it 2.062 r_scbond_other 2.032 r_mcbond_it 1.989 r_mcbond_other 1.987 r_angle_refined_deg 1.557 r_angle_other_deg 1.234 r_symmetry_nbd_refined 0.237 r_nbd_other 0.22 r_ext_dist_refined_d 0.211 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.153 r_ncsr_local_group_1 0.144 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing