Navigation Tabs Crystal structure of FutA after an accumulated dose of 5 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 2.13 42.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.718 α = 90 b = 78.66 β = 97.788 c = 48.382 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 294 PIXEL DECTRIS PILATUS3 6M 2018-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968 Diamond I24
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
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.76 40.97 100 0.931 0.923 0.235 3.1 26.23 29256
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 0.93 0.431 0.684 0.41 19.1
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 1.76 40.97 29256 1503 99.956 0.204 0.2017 0.21 0.2413 0.24 31.339
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] 0.187 -0.219 -0.089 -0.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.678 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 14.53 r_dihedral_angle_1_deg 6.515 r_lrange_other 5.95 r_lrange_it 5.948 r_scangle_it 4.547 r_scangle_other 4.546 r_mcangle_it 2.889 r_mcangle_other 2.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.678 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 14.53 r_dihedral_angle_1_deg 6.515 r_lrange_other 5.95 r_lrange_it 5.948 r_scangle_it 4.547 r_scangle_other 4.546 r_mcangle_it 2.889 r_mcangle_other 2.889 r_scbond_it 2.835 r_scbond_other 2.834 r_mcbond_it 1.871 r_mcbond_other 1.862 r_angle_refined_deg 1.413 r_angle_other_deg 1.202 r_symmetry_nbd_refined 0.22 r_nbd_other 0.201 r_nbd_refined 0.185 r_symmetry_nbd_other 0.178 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.15 r_metal_ion_refined 0.106 r_symmetry_xyhbond_nbd_refined 0.1 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.059 r_ext_dist_refined_d 0.029 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2462 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction cctbx.prime data scaling MOLREP phasing
