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TR-SFX MmCPDII-DNA complex: 6 ns snapshot. Includes 6 ns, dark, and extrapolated structure factors
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YC7 7YC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.6 296 100 mM Sodium Acetate pH 4.6
250 mM ammonium sulfate
4% PEG4000 (w/v)
50 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.47 α = 90 b = 115.93 β = 90 c = 169.35 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL PSI JUNGFRAU 16M 2021-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SwissFEL ARAMIS BEAMLINE ESA 1.0875 SwissFEL ARAMIS ESA
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) 100 undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 71654 71654
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 SwissFEL injector 4.2 (µl/min) undefined (µm)
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 2.1 16.78 99.99 0.996 10.37 902.4 83878
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 2.1 2.12 100 0.517 1.89
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7YC7 2.2 16.78 72968 3576 99.99 0.2282 0.2273 0.2458 0.2144
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.138 f_angle_d 0.8 f_chiral_restr 0.176 f_bond_d 0.022 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7056 Nucleic Acid Atoms 1004 Solvent Atoms 369 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction pointless data scaling REFMAC phasing