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TR-SMX closed state structure (0-5ms) of bacteriorhodopsin
Serial Crystallography (SX)
Serial Crystallography (SX)
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B6Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.6 294 100 mM Na/K Phosphate buffer pH 5.6 30 % PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62 α = 90 b = 62 β = 90 c = 110.3 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS EIGER X 16M 2018-07-22 M SINGLE WAVELENGTH 2 1 x-ray 298 PIXEL DECTRIS EIGER X 16M 2018-07-22 M SINGLE WAVELENGTH 3 1 x-ray 298 PIXEL DECTRIS EIGER X 16M 2018-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA 2 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA 3 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection 2 injection 3 injection
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 high viscosity injector undefined (µl/min) undefined (µm) glass capillary LCP 2 undefined (µl/min) undefined (µm) flass capillary LCP
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 3 2.1 38.5 100 0.99 0.034 13.3 984.9 13882
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) 3 2.1 2.18 100 0.52 0.86 1.33 24.6
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 THROUGHOUT 5B6Z 2.6 38.47 0.02 6737 419 90.82 0.2529 0.2494 0.2534 0.3012 0.2983 83.73
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 9.8572 f_angle_d 0.447 f_chiral_restr 0.0347 f_plane_restr 0.003 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1790 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling