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Magnetic effects of thaumatin crystals; observation of the crystal growth of magneto-Archimedes levitation and magnetic orientation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.5 293 84 mM ADA pH 6.5, 42 mM GdCl3, 0.51 M NaK-tartrate, 0.017 % NaN3
Crystal Properties Matthews coefficient Solvent content 2.87 56.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.083 α = 90 b = 58.083 β = 90 c = 150.47 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 PIXEL DECTRIS PILATUS 6M 2023-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.775 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 0.99 45.98 99 0.026 0.998 20.6 8.2 145471 8.176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1 100 0.314 0.93 3.5 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 0.99 37.99 138147 7248 99.8 0.12639 0.12598 0.1304 0.13382 0.137 RANDOM 11.856
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] -0.17 -0.17 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.787 r_dihedral_angle_4_deg 16.483 r_dihedral_angle_3_deg 11.706 r_dihedral_angle_1_deg 7.099 r_long_range_B_refined 2.699 r_rigid_bond_restr 2.122 r_long_range_B_other 2.115 r_angle_refined_deg 1.92 r_angle_other_deg 1.596 r_scangle_other 1.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.787 r_dihedral_angle_4_deg 16.483 r_dihedral_angle_3_deg 11.706 r_dihedral_angle_1_deg 7.099 r_long_range_B_refined 2.699 r_rigid_bond_restr 2.122 r_long_range_B_other 2.115 r_angle_refined_deg 1.92 r_angle_other_deg 1.596 r_scangle_other 1.587 r_mcangle_it 1.354 r_mcangle_other 1.354 r_scbond_it 1.239 r_scbond_other 1.239 r_mcbond_it 0.93 r_mcbond_other 0.926 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1545 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing