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X-ray structure of the adduct between thaumatin and cisplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QY5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 20 % PEG3350, 0.2 M sodium tartrate. Crystals of the adduct were obtained by soaking procedure, adding 1 uL of cisplatin solution 10 mM to the drop containing thaumatin crystals
Crystal Properties Matthews coefficient Solvent content 2.82 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.837 α = 90 b = 57.837 β = 90 c = 150.159 γ = 90
Symmetry Space Group P 41 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 2016-02-03 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 1.45 53.98 94.8 0.057 40 7 43868
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 68 0.466 1.7 1.4
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 (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 3QY5 1.45 53.97 41675 2147 94.89 0.11444 0.1124 0.1149 0.15369 0.1556 RANDOM 22.169
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] 0.4 0.4 -0.79
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.27 r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 21.379 r_sphericity_bonded 18.377 r_dihedral_angle_3_deg 12.101 r_rigid_bond_restr 9.57 r_dihedral_angle_1_deg 6.984 r_long_range_B_refined 6.356 r_scbond_it 5.048 r_mcangle_it 2.934
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.27 r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 21.379 r_sphericity_bonded 18.377 r_dihedral_angle_3_deg 12.101 r_rigid_bond_restr 9.57 r_dihedral_angle_1_deg 6.984 r_long_range_B_refined 6.356 r_scbond_it 5.048 r_mcangle_it 2.934 r_angle_refined_deg 2.904 r_mcbond_it 2.73 r_chiral_restr 0.264 r_bond_refined_d 0.037 r_gen_planes_refined 0.017 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1551 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing