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MicroED structure of proteinase K from a 325 nm thick lamella measured at 120 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 = 66.781 α = 90 b = 66.781 β = 90 c = 99.215 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 2020-12-11
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 2.7 20 82.6 0.64 0.708 0.296 0.893 3.2 5.5 30326 23.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.86 83 1.765 1.951 0.359
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 2.7 19.43 1.34 5453 347 83.02 0.2442 0.2413 0.2852 14.5
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 5.7021 f_angle_d 0.6556 f_chiral_restr 0.0435 f_bond_d 0.0042 f_plane_restr 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2029 Nucleic Acid Atoms Solvent Atoms 15 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 66.781 Length b 66.781 Length c 66.781 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 15 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 TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode DIFFRACTION Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 120 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