Navigation Tabs SSX structure of Thaumatin grown in batch conditions
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 BATCH MODE 6.5 294 Thaumatin from Thaumatococcus danielii (T7639, Sigma-Aldrich) was dissolved in milliQ water to a final concentration of 50 mg/mL. Thaumatin solution was mixed in a 1:1 ratio with a precipitant solution containing 40% (w/v) sodium potassium tartrate, 0.1 M bis-Tris propane pH 6.5 in a 1 mL Eppendorf tube at 21 degrees before vortexing for 10 seconds.
Crystal Properties Matthews coefficient Solvent content 2.99 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.97 α = 90 b = 58.97 β = 90 c = 152.55 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 35295 28964 35295
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 1.68 58.97 100 0.987 0.115 6.4 412.89 31714 22.56
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 1.68 1.71 100 0.425 1.701 265.02
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 1.68 55.064 31628 1554 99.994 0.17 0.1686 0.1776 0.1923 0.2053 29.58
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] -2.341 -2.341 4.682
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.406 r_lrange_other 18.299 r_scangle_it 14.927 r_scangle_other 14.924 r_dihedral_angle_6_deg 14.552 r_dihedral_angle_3_deg 10.906 r_scbond_it 10.399 r_scbond_other 10.394 r_mcangle_other 10.16 r_mcangle_it 10.144
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.406 r_lrange_other 18.299 r_scangle_it 14.927 r_scangle_other 14.924 r_dihedral_angle_6_deg 14.552 r_dihedral_angle_3_deg 10.906 r_scbond_it 10.399 r_scbond_other 10.394 r_mcangle_other 10.16 r_mcangle_it 10.144 r_rigid_bond_restr 7.799 r_mcbond_it 7.281 r_mcbond_other 7.202 r_dihedral_angle_1_deg 6.846 r_dihedral_angle_2_deg 5.783 r_angle_refined_deg 1.218 r_angle_other_deg 0.445 r_symmetry_nbd_refined 0.254 r_nbd_other 0.237 r_symmetry_nbd_other 0.194 r_nbd_refined 0.184 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.105 r_symmetry_xyhbond_nbd_refined 0.084 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.065 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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
