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The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and oxaliplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT pdb code 1JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 RNase A was crystallized at room temperature mixing 1 L solution of protein at 20 mg mL-1 with an equal volume of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. Two weeks after their appearance, single crystals were soaked for four days in a solution of Oxaliplatin dissolved in 10 L of reservoir. At the final, Pt drugs:protein concentrations were in 10:1 ratio, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.722 α = 90 b = 32.736 β = 90.36 c = 73.233 γ = 90
Symmetry Space Group C 1 2 1
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+ mirrors 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 2.27 50 95.4 0.161 6.6 10764 10764
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb code 1JVT 2.27 50 10237 10237 520 94.27 0.22825 0.22825 0.22451 0.228 0.30092 0.2991 RANDOM 46.399
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] -1.21 0.76 -0.55 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.39 r_dihedral_angle_3_deg 14.695 r_dihedral_angle_4_deg 10.413 r_long_range_B_refined 7.355 r_long_range_B_other 7.343 r_dihedral_angle_1_deg 6.609 r_mcangle_it 4.941 r_mcangle_other 4.939 r_scangle_other 4.859 r_scbond_it 3.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.39 r_dihedral_angle_3_deg 14.695 r_dihedral_angle_4_deg 10.413 r_long_range_B_refined 7.355 r_long_range_B_other 7.343 r_dihedral_angle_1_deg 6.609 r_mcangle_it 4.941 r_mcangle_other 4.939 r_scangle_other 4.859 r_scbond_it 3.393 r_scbond_other 3.388 r_mcbond_it 3.209 r_mcbond_other 3.206 r_angle_refined_deg 2.53 r_angle_other_deg 1.08 r_chiral_restr 0.091 r_gen_planes_refined 0.033 r_bond_refined_d 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 1835 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 34
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling