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Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 18 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 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.72 α = 69.96 b = 49.05 β = 68.59 c = 49.31 γ = 77
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 2018-03-16 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 23.23 86.9 0.06 0.958 8.8 2.3 17918
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 92.4 0.152 0.939 3.9 1.9
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 2.004 23.228 17918 894 86.874 0.185 0.1827 0.1869 0.2241 0.232 22.264
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] 0.233 0.286 0.182 -0.056 1.707 0.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.838 r_dihedral_angle_3_deg 18.598 r_dihedral_angle_4_deg 16.465 r_lrange_it 9.099 r_lrange_other 9.093 r_dihedral_angle_1_deg 6.959 r_scangle_it 4.046 r_scangle_other 3.99 r_mcangle_other 3.522 r_mcangle_it 3.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.838 r_dihedral_angle_3_deg 18.598 r_dihedral_angle_4_deg 16.465 r_lrange_it 9.099 r_lrange_other 9.093 r_dihedral_angle_1_deg 6.959 r_scangle_it 4.046 r_scangle_other 3.99 r_mcangle_other 3.522 r_mcangle_it 3.521 r_scbond_it 2.469 r_scbond_other 2.439 r_mcbond_it 2.093 r_mcbond_other 2.092 r_angle_refined_deg 1.616 r_angle_other_deg 1.246 r_ext_dist_refined_d 0.3 r_nbd_other 0.218 r_nbd_refined 0.205 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.154 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing