Navigation Tabs High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle, 33 ms structure
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 293 0.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4000, 15% v/v Glycerol (cryo-screen solution) and 3 % w/v Benzamidine Hydrochloride mixed with 60 mg/mL protein (3:2) protein to mother liquor ratio
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( ? ) Angle ( ? ) a = 83.69 ¦Á = 90 b = 83.4 ¦Â = 107.63 c = 86.87 ¦Ã = 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 CCD MPCCD 2019-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.38 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Folded in Nuclear Grade Grease injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 41817 89389 41817
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 viscous jet extrusion 4 (?l/min) undefined (?m) HPLC nuclear grade grease
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 2.1 25 100 0.994 0.094 7.6 449.4 68919
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 2.1 2.14 100 0.31 1.12 203
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 R-Free R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6PTQ 2.4 24.33 36457 1792 85.53 0.29435 0.29241 0.33349 RANDOM 22.116
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] 0.8 0.32 -0.57 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_3_deg 28.073 r_dihedral_angle_4_deg 20.299 r_dihedral_angle_1_deg 12.277 r_long_range_B_other 6.118 r_long_range_B_refined 6.115 r_mcangle_it 3.067 r_mcangle_other 3.067 r_scangle_other 2.393 r_angle_refined_deg 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_3_deg 28.073 r_dihedral_angle_4_deg 20.299 r_dihedral_angle_1_deg 12.277 r_long_range_B_other 6.118 r_long_range_B_refined 6.115 r_mcangle_it 3.067 r_mcangle_other 3.067 r_scangle_other 2.393 r_angle_refined_deg 2.12 r_mcbond_it 1.87 r_mcbond_other 1.868 r_scbond_it 1.419 r_scbond_other 1.419 r_angle_other_deg 1.233 r_chiral_restr 0.21 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7320 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling REFMAC phasing
