Navigation Tabs SSX structure of Thaumatin grown in microfluidic droplets
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROFLUIDIC 6.5 294 Crystals were grown in a droplet microfluidic device 50 x 40 micron (w x h) with a QX200 oil flow rate of 22.5 uL/min, a crystallisation condition flow rate of 6 uL/min and a thaumatin flow rate of 1.5 uL/min resulting in 81 pL droplets.
Thaumatin from Thaumatococcus danielii (T7639, Sigma-Aldrich) was dissolved in milliQ water to a final concentration of 50 mg/mL
The crystallisation condition was 40% (w/v) sodium potassium tartrate, 0.1 M bis-Tris propane pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.99 59.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.97 α = 90 b = 58.97 β = 90 c = 152.75 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 293 PIXEL PSI JUNGFRAU 4M 2025-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 SOS Chip fixed target
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 19053 17659 19053
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.6 58.97 100 0.99 0.095 7.1 224.12 36626 20.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.314 2.024 0.5 94.16
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 1.6 55.073 36538 1860 100 0.147 0.1457 0.1465 0.1758 0.18 29.453
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] -2.105 -2.105 4.21
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.626 r_lrange_other 19.619 r_scangle_other 17.214 r_scangle_it 17.213 r_dihedral_angle_6_deg 15.867 r_scbond_it 12.155 r_scbond_other 12.155 r_dihedral_angle_3_deg 11.35 r_mcangle_other 10.735 r_mcangle_it 10.714
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.626 r_lrange_other 19.619 r_scangle_other 17.214 r_scangle_it 17.213 r_dihedral_angle_6_deg 15.867 r_scbond_it 12.155 r_scbond_other 12.155 r_dihedral_angle_3_deg 11.35 r_mcangle_other 10.735 r_mcangle_it 10.714 r_mcbond_it 7.808 r_mcbond_other 7.752 r_dihedral_angle_1_deg 6.979 r_rigid_bond_restr 6.709 r_dihedral_angle_2_deg 6.297 r_angle_refined_deg 1.677 r_angle_other_deg 0.612 r_symmetry_xyhbond_nbd_refined 0.261 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.196 r_nbd_refined 0.194 r_nbtor_refined 0.175 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing
