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SFX structure of the class II photolyase complexed with a thymine dimer
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZCW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.6 293 100 mM Amm sulfate, 100 mM Acetate pH 4.6, 4% PEG 4000, 10 mM Tris pH 7.5, 75 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.2 α = 90 b = 117.76 β = 90 c = 170.47 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 293 PIXEL PSI JUNGFRAU 16M KB 2022-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SwissFEL ARAMIS BEAMLINE ESA 1.035 SwissFEL ARAMIS ESA
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Viscous Injector injection
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 Viscous Injector undefined (µl/min) undefined (µm) cellulose
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 2 32.46 99.998961 0.9985686 0.0389 22.919011 6068.312898 96204 35.72
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) 2.0346 2.0717 100 0.066937 2.856 0.36 463.3 4755
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.11 32.46 1.33 66097 3330 80.35 0.1618 0.16 0.1604 0.1962 0.1969 53.01
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 19.8247 f_angle_d 0.9951 f_chiral_restr 0.0531 f_plane_restr 0.0106 f_bond_d 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7212 Nucleic Acid Atoms 1118 Solvent Atoms 288 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing