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X.ray structure of the oxaliplatin/beta-lactoglobulin adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZSR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.2M KCl, 0.04M HEPES, 35% v/v pentaerythritol propoxylate
Crystal Properties Matthews coefficient Solvent content 1.86 33.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.87 α = 90 b = 112.58 β = 117.637 c = 38.08 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
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 2.01 56.3 86.9 0.06 0.958 8.8 2.3 17918 19.3
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 2.01 56.3 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 6ZSR 2.01 56.3 17379 772 97.635 0.216 0.2123 0.2177 0.2845 0.2836 24.961
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] -0.105 -0.076 0.054 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.574 r_dihedral_angle_3_deg 18.696 r_dihedral_angle_4_deg 8.786 r_dihedral_angle_1_deg 7.398 r_lrange_it 6.122 r_lrange_other 6.122 r_scangle_it 4.093 r_scangle_other 4.092 r_mcangle_it 3.337 r_mcangle_other 3.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.574 r_dihedral_angle_3_deg 18.696 r_dihedral_angle_4_deg 8.786 r_dihedral_angle_1_deg 7.398 r_lrange_it 6.122 r_lrange_other 6.122 r_scangle_it 4.093 r_scangle_other 4.092 r_mcangle_it 3.337 r_mcangle_other 3.337 r_scbond_it 2.492 r_scbond_other 2.486 r_mcbond_it 2.071 r_mcbond_other 2.067 r_angle_refined_deg 1.532 r_angle_other_deg 1.174 r_nbd_other 0.239 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.194 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.163 r_nbtor_refined 0.15 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2521 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOSFLM data scaling PHASER phasing