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Structure of PAS-GAF fragment of Deinococcus phytochrome by serial femtosecond crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9C PDB 2O9C lacking the bilin and all neighboring side chains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.6 298 PEG 3350, isopropanol, glycerol, sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.535 α = 90 b = 53.385 β = 116.32 c = 80.912 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RAYONIX MX170-HS Compound refractive lenses 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.265 SLAC LCLS MFX
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 1.65 72.5 99.97 0.968 62.83 72.62 41877
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 1.65 1.709 99.93 0.087 2.414 17.05
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 2O9C lacking the bilin and all neighboring side chains 1.65 32.243 1.35 41718 1925 99.81 0.1737 0.1723 0.1733 0.2026 0.2034 42.0992
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 20.909 f_angle_d 0.954 f_chiral_restr 0.054 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2468 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 50
Software Software Software Name Purpose cctbx.xfel data collection cctbx.prime data reduction cctbx.xfel data reduction PHASER phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction psana data reduction cctbx.prime data scaling