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Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure
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% PEG500DM
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
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 2.4 39.41 100 0.9925 0.089 6.61 159.5 16730
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 2.4 2.441 100 0.4237 1.2569 0.87 38.1
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 2.5 14.96 11400 592 80.96 0.4089 0.4048 0.4065 0.4869 0.4892 RANDOM 49.273
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] 1.89 -4.28 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.894 r_dihedral_angle_3_deg 19.844 r_dihedral_angle_4_deg 19.411 r_dihedral_angle_1_deg 5.785 r_angle_refined_deg 1.478 r_angle_other_deg 1.213 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.894 r_dihedral_angle_3_deg 19.844 r_dihedral_angle_4_deg 19.411 r_dihedral_angle_1_deg 5.785 r_angle_refined_deg 1.478 r_angle_other_deg 1.213 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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