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MicroED structure of proteinase K from a 540 nm thick lamella measured at 200 kV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CL7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.72 α = 90 b = 67.72 β = 90 c = 102.85 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 2020-11-14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 32 78.6 0.325 0.386 0.156 0.925 3.26 3.3 47088 19.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.45 2.49 79.4 1.057 0.486
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-Free (Depositor) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 6CL7 2.4 32.16 1.34 7619 388 77.15 0.1945 0.193 0.222 15.78
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 6.1975 f_angle_d 0.872 f_chiral_restr 0.0528 f_bond_d 0.006 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2029 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument LEICA PLUNGER Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 67.72 Length b 67.72 Length c 67.72 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (6CL7) Refinement Space RECIPROCAL Refinement Protocol RIGID BODY FIT Refinement Target Maximum liklihood Overall B Value 16 Fitting Procedure Details
Data Acquisition Detector Type FEI CETA (4k x 4k) Electron Dose (electrons/Å**2) 0.01
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA 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) 200 Imaging Details
EM Software Task Software Package Version MODEL FITTING Coot CRYSTALLOGRAPHY MERGING AIMLESS RECONSTRUCTION PHENIX MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE