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RT XFEL structure of CypA solved using MESH injection system
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YUM PDB entry 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 56.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.01 α = 90 b = 52.61 β = 90 c = 89.32 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 RAYONIX MX170-HS 2016-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.32 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 MESH (Sierra et al, 2012) injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 50 (fs) 10 undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 18358 18358
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 1.62 20 99.95 0.993 0.083 5.312 224.08 26445 20.21
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 1.62 1.65 0.865 0.284 0.747
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4YUM 1.62 19.91 1.34 26445 832 99.98 0.1369 0.1362 0.1379 0.1569 0.1585 26.29
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 14.9854 f_angle_d 0.8453 f_chiral_restr 0.0573 f_bond_d 0.0052 f_plane_restr 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1249 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data collection DIALS data reduction DIALS data scaling PHASER phasing