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Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.9 293 100 mM MES, pH 6.9, 100 mM Na formate, and 30% PEG500DME
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.8 α = 90 b = 142.2 β = 90 c = 94.7 γ = 90
Symmetry Space Group C 2 2 21
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 2016-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.77 SACLA BL3
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
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 47.35 100 0.9962 0.061 9.64 561.2 18961
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 2.3 2.34 100 0.8421 0.6049 1.55 138.5
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 3UG9 2.3 15 17940 901 99.43 0.1843 0.182 0.1917 0.2322 0.2394 RANDOM 67.069
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] 1.58 -5.49 3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 19.455 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_1_deg 5.827 r_angle_refined_deg 1.393 r_angle_other_deg 1.314 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 19.455 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_1_deg 5.827 r_angle_refined_deg 1.393 r_angle_other_deg 1.314 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling PHASER phasing