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Photoactivation in Bacteriophytochromes, reference (dark) structure for the 3 ps time point
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 291 Hampton Crystal Screen Cryo HR2-122, #9 (PEG 4000), benzamidine HCl (3%)
Crystal Properties Matthews coefficient Solvent content 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.58 α = 90 b = 83.04 β = 107.74 c = 86.79 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 293 PIXEL SLAC ePix10k 2M 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.3 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Superlube (viscous media) injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 120 5 9.3 (KeV)
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 viscous media injector undefined (µl/min) undefined (µm)
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 2.3 30.5 100 0.99 0.095 5.8 963 50738 63.63
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 2.3 2.43 100 0.11 0.22 664
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 FOURIER SYNTHESIS FREE R-VALUE 2.3 27.3 0.03 43709 2222 86.78 0.1939 0.1908 0.1908 0.2509 0.2509 74.67
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 17.5316 f_angle_d 1.0997 f_chiral_restr 0.0497 f_plane_restr 0.0111 f_bond_d 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7322 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling Coot model building