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Structure of lysozyme by continuous serial electron diffraction (SerialED)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SKW
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.66 α = 87.73 b = 31.15 β = 108.97 c = 33.57 γ = 111.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY FREE R-VALUE 0.83 11.73 1.96 87855 2000 98.29 0.1762 0.1755 0.2094 0.2064 0.2282 Random selection 11.04
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 6.3402 f_angle_d 1.2195 f_chiral_restr 0.1137 f_bond_d 0.0188 f_plane_restr 0.0113
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 992 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 7
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details Manual blotting in room temperature with ambient humidity
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 0.83 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 26.66 Length b 31.15 Length c 31.15 Angle Alpha 111.6 Angle Beta 108.97 Angle Gamma 111.6
Map-Model Fitting and Refinement Id 1 (7SKW) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target maximum-likelihood Overall B Value 11.04 Fitting Procedure Details
Data Acquisition Detector Type FEI CETA (4k x 4k) Electron Dose (electrons/Å**2) 1.52
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version RECONSTRUCTION PHENIX MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE