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PAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps after photoexcitation
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.95 298 60 mM Sodium Acetate, 3.3% PEG400, 1 mM DTT, 30% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.45 49.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.98 α = 90 b = 116.69 β = 90 c = 117.86 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 298 CCD MPCCD 2018-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.7712 SACLA BL3
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 grease jet injection
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 undefined (µl/min) undefined (µm) Superlube
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 2.21 41.46 100 0.98 0.1059 6.1 106.11 39316
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 2.21 2.25 100 0.38 1.1464 0.88 34.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K5B 2.21 36.94 33150 1829 90.21 0.2317 0.2304 0.2323 0.2562 0.2556 RANDOM 78.626
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] -0.33 -0.99 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_3_deg 15.067 r_dihedral_angle_4_deg 12.454 r_dihedral_angle_1_deg 5.846 r_angle_refined_deg 1.152 r_angle_other_deg 0.899 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_3_deg 15.067 r_dihedral_angle_4_deg 12.454 r_dihedral_angle_1_deg 5.846 r_angle_refined_deg 1.152 r_angle_other_deg 0.899 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4794 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 86
Software Software Software Name Purpose CrystFEL data reduction CrystFEL data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction