Navigation Tabs SFX structure of FutA after an accumulated dose of 350 kGy
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 294 Purified protein, diluted crystal seeds, and crystallisation buffer were mixed at a 1:1.5:1.5 ratio. Crystallisation buffer was 25% PEG 3350, 200 mM sodium thiocyanate. Crystal seed stock was diluted 1:20 in 25% PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.08 40.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.366 α = 90 b = 78.22 β = 97.903 c = 48.025 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD MPCCD 2022-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.126 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Silicon nitride chip 25600 apertures
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 undefined (KeV)
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 1.65 32.441 100 0.97 0.134 3.7 165.2 34653 20.98
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 1.65 1.679 100 0.691 0.4 0.43 82.4
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 1.65 32.441 34653 1786 99.957 0.161 0.1599 0.17 0.1885 0.2 27.641
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] 0.295 -0.303 0.161 -0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.86 r_dihedral_angle_3_deg 12.708 r_lrange_it 7.073 r_lrange_other 7.071 r_dihedral_angle_1_deg 6.182 r_scangle_it 6.13 r_scangle_other 6.129 r_dihedral_angle_2_deg 5.619 r_scbond_it 3.834 r_scbond_other 3.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.86 r_dihedral_angle_3_deg 12.708 r_lrange_it 7.073 r_lrange_other 7.071 r_dihedral_angle_1_deg 6.182 r_scangle_it 6.13 r_scangle_other 6.129 r_dihedral_angle_2_deg 5.619 r_scbond_it 3.834 r_scbond_other 3.831 r_mcangle_it 2.842 r_mcangle_other 2.841 r_mcbond_it 2.019 r_mcbond_other 2.002 r_angle_refined_deg 1.572 r_angle_other_deg 0.538 r_symmetry_nbd_refined 0.277 r_nbd_refined 0.221 r_nbd_other 0.205 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.144 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.007 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 2460 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction cctbx.xfel.merge data scaling MOLREP phasing
