☰ Navigation Tabs
Acoustofluidic Sample Delivery System for Serial Crystallography, Thaumatin with acoustic ON
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROFLUIDIC 273 100 mg of Thaumatin from Thaumatococcus daniellii (Sigma, T7638) was dissolved in 1 mL of MiliQ water, reaching a concentration of 100 mg/mL with solutions vortexed to ensure complete dissolution. Subsequently, 200 uL of the thaumatin solution was mixed with 200 uL of 1.6 M (Na, K, tartrate) crystallization solution. A tube of the resulting mixture was placed on a rotator operating at 20 C. After an incubation period of 16-18 hr, thaumatin crystals grow to a size of 15-20 um with high density. Crystals were stored at 4 C until the experiment.
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.61 α = 90 b = 58.61 β = 90 c = 151.7 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 273 PIXEL DECTRIS EIGER2 X 9M 2024-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE MicroMAX 0.9537 MAX IV MicroMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 8.13 100 0.9929637 7.037744 444 25123
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 0.6345607
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 8.13 25059 1267 98.642 0.159 0.1569 0.1569 0.1923 0.1923 28.931
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] 0.324 0.324 -0.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.207 r_dihedral_angle_3_deg 13.713 r_dihedral_angle_2_deg 9.02 r_lrange_it 8.816 r_scangle_it 8.341 r_dihedral_angle_1_deg 7.545 r_scbond_it 5.794 r_mcangle_it 4.492 r_mcbond_it 3.309 r_angle_refined_deg 2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.207 r_dihedral_angle_3_deg 13.713 r_dihedral_angle_2_deg 9.02 r_lrange_it 8.816 r_scangle_it 8.341 r_dihedral_angle_1_deg 7.545 r_scbond_it 5.794 r_mcangle_it 4.492 r_mcbond_it 3.309 r_angle_refined_deg 2.32 r_symmetry_xyhbond_nbd_refined 0.495 r_nbtor_refined 0.302 r_xyhbond_nbd_refined 0.25 r_nbd_refined 0.19 r_chiral_restr 0.165 r_symmetry_nbd_refined 0.152 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1550 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing