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First Crystal Structure for an Oxaliplatin-Protein Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J1A PDB code 4J1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 293 Crystals of HEWL in the presence of Oxaliplatin (protein to metal drug ratio 1:10, incubation time=24 h) have been grown by hanging drop vapour diffusion method using a reservoir solution of 0.6 M NaNO3, 0.1 M sodium acetate pH 4.4 and 20 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.049 α = 90 b = 77.049 β = 90 c = 37.287 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+ mirrors 2013-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.729 54.48 97.8 0.088 3.7 12001 12001
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB code 4J1A 1.73 54.48 11406 570 97.89 0.182 0.18109 0.18 0.1912 0.235 0.2333 RANDOM 26.551
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] -1.18 -1.18 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.717 r_dihedral_angle_4_deg 21.301 r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 6.528 r_long_range_B_refined 6.392 r_long_range_B_other 6.311 r_scangle_other 5.066 r_scbond_it 3.563 r_scbond_other 3.479 r_mcangle_other 2.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.717 r_dihedral_angle_4_deg 21.301 r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 6.528 r_long_range_B_refined 6.392 r_long_range_B_other 6.311 r_scangle_other 5.066 r_scbond_it 3.563 r_scbond_other 3.479 r_mcangle_other 2.881 r_mcangle_it 2.879 r_mcbond_it 2.201 r_mcbond_other 2.187 r_angle_refined_deg 1.852 r_angle_other_deg 0.986 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing