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RT XFEL structure of CypA solved using celloluse carrier media
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 291 100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.8 56.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43 α = 90 b = 52.6 β = 90 c = 89.2 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 291 CCD MPCCD 2017-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.24 SACLA BL3
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Cellulose (Sugahara et al., 2017) injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 23947 23947
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 1.56 20 100 0.993 0.0794 7.91 261 29527 24.82
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 1.56 1.58 100 0.586 0.66 1.46 40.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YUM 1.56 19.9 1.35 29527 929 99.99 0.1353 0.1348 0.1509 0.1841 29.62
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 16.5416 f_angle_d 1.2979 f_chiral_restr 0.0814 f_bond_d 0.0151 f_plane_restr 0.0093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1249 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data collection DIALS data reduction DIALS data scaling PHASER phasing