DOI: 10.5061/dryad.73n5tb354
title: Data from: Correction of preferred-orientation induced distortion in cryo-electron microscopy maps

description: Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit
 distortion when the cryo-EM dataset is incomplete, usually caused by
 unevenly distributed orientations. Prior efforts had been attempted to
 address this preferred orientation problem using tilt-collection strategy,
 modifications to grids or to air-water-interfaces. However, these
 approaches often require time-consuming experiments and the effect was
 always protein dependent. Here, we developed a procedure containing
 removing mis-aligned particles and an iterative reconstruction method
 based on signal-to-noise ratio of Fourier component to correct such
 distortion by recovering missing data using a purely computational
 algorithm. This procedure called Signal-to-Noise Ratio Iterative
 Reconstruction Method (SIRM) was applied on incomplete datasets of various
 proteins to fix distortion in cryo-EM maps and to a more isotropic
 resolution. In addition, SIRM provides a better reference map for further
 reconstruction refinements, resulting in an improved alignment, which
 ultimately improves map quality and benefits model building.
description: # SIRM: Open Source Data --- We have submitted the original chart files
 (.csv) and density maps (.mrc) related to the images in the article
 "Correction of preferred-orientation induced distortion in
 cryo-electron microscopy maps" ## Descriptions ###
 SIRM\_Fig1\_csv.rar * *Fig1A.csv*: The CSV file corresponding to the
 histogram of Euler angle deviations in particle sets with different
 degrees of missing wedge under conventional refinement. * *Fig1B.csv*: The
 CSV file corresponding to the histogram of Euler angle deviations in
 particle sets with different degrees of missing wedge After
 Cross-Validation process. ### SIRM\_Fig3\_MRC\_map.rar *
 *groundTruth.mrc*: The ground-truth density map of Apo-ferritin without
 missing cone, corresponding to Fig.3A. * *loss70_sameParticleNum.mrc*: The
 MC-35 density map of Apo-ferritin, corresponding to Fig.3D. *
 *loss70_sameParticleNum_SIRM.mrc*: The MC-35 density map of Apo-ferritin
 after SIRM processing, corresponding to Fig.3G. *
 *loss80_sameParticleNum.mrc*: The MC-40 density map of Apo-ferritin,
 corresponding to Fig.3E. * *loss80_sameParticleNum_SIRM.mrc*: The MC-40
 density map of Apo-ferritin after SIRM processing, corresponding to
 Fig.3H. * *loss90_sameParticleNum.mrc*: The MC-45 density map of
 Apo-ferritin, corresponding to Fig.3F. *
 *loss90_sameParticleNum_SIRM.mrc*: The MC-45 density map of Apo-ferritin
 after SIRM processing, corresponding to Fig.3I. ###
 SIRM\_Fig4\_MRC\_map.rar * *groundTruth.mrc*: The ground-truth density map
 of EMPIAR-10097 HA-trimer without missing cone, corresponding to Fig.4A. *
 *loss70_sameParticleNum_bf50.mrc*: The MC-35 density map of EMPIAR-10097
 HA-trimer, corresponding to Fig.4D. * *loss70_SIRM_hist10_bf50.mrc*: The
 MC-35 density map of EMPIAR-10097 HA-trimer after SIRM processing,
 corresponding to Fig.4G. * *loss80_sameParticleNum_bf50.mrc*: The MC-35
 density map of EMPIAR-10097 HA-trimer, corresponding to Fig.4E. *
 *loss80_SIRM_hist10_bf50.mrc*: The MC-35 density map of EMPIAR-10097
 HA-trimer after SIRM processing, corresponding to Fig.4H. *
 *loss90_sameParticleNum_bf50.mrc*: The MC-35 density map of EMPIAR-10097
 HA-trimer, corresponding to Fig.4F. * *loss90_SIRM_hist10_bf50.mrc*: The
 MC-35 density map of EMPIAR-10097 HA-trimer after SIRM processing,
 corresponding to Fig.4I. ###
 SIRM\_Fig6&\&FigS8&\&FigS9\_\_csv\&MRC.rar *
 *Fig6A.csv*: The CSV file corresponding to the Fig.6A, The histogram
 compares the Euler angle errors between conventional refinement and SIRM
 refinement, as well as between cross-validation and mask-picking. *
 *Fig6B.csv*: The CSV file corresponding to the Fig.6B. Note that this CSV
 file contains several columns, which represent multiple directional FSCs.
 * *FigS8A.csv*: The CSV file corresponding to the FigS.8A. This histogram
 shows the directional-FSC of ribosomes after SIRM processing. *
 *FigS8B.csv*: The CSV file corresponding to the FigS.8A. This histogram
 shows the directional-FSC of ribosomes without SIRM processing. *
 *FigS8E.csv*: The CSV file corresponding to the Fig.S8E. Note that this
 CSV file contains several columns, which represent multiple directional
 FSCs. * *ribosome_MC50.mrc*: The MC-45 density map of ribosome with
 alignment-error, corresponding to Fig.6C. * *ribosome_SIRM.mrc*: The MC-45
 density map of ribosome with alignment-error after SIRM processing,
 corresponding to Fig.6D. ### SIRM\_Fig7&\&FigS12\_csv.rar *
 *FigS12C.csv FigS12D.csv FigS12E.csv FigS12F.csv*: The CSV file
 corresponding to FigS12C FigS12D FigS12E FigS12F. ### SIRM\_FigS5\_csv.rar
 * *FigS5A.csv FigS5C.csv FigS5E.csv FigS5G.csv FigS5I.csv FigS5K.csv*: The
 3D-FSC CSV file corresponding to FigS5A FigS5C FigS5E FigS5G FigS5I
 FigS5K. Note that this CSV file contains several columns, which represent
 multiple directional FSCs * *FigS5B.csv FigS5D.csv FigS5F.csv FigS5H.csv
 FigS5J.csv FigS5L.csv*: The D-FSC CSV file corresponding to FigS5A FigS5C
 FigS5E FigS5G FigS5I FigS5K. ### SIRM\_FigS6\_csv.rar * *FigS6A.csv
 FigS6C.csv FigS6E.csv FigS6G.csv FigS6I.csv FigS6K.csv*: The 3D-FSC CSV
 file corresponding to FigS6A FigS6C FigS6E FigS6G FigS6I FigS6K. Note that
 this CSV file contains several columns, which represent multiple
 directional FSCs * *FigS6B.csv FigS6D.csv FigS6F.csv FigS6H.csv FigS6J.csv
 FigS6L.csv*: The D-FSC CSV file corresponding to FigS6A FigS6C FigS6E
 FigS6G FigS6I FigS6K. ### SIRM\_FigS10&\&FigS11\_csv.rar *
 *FigS11A.csv FigS11B.csv FigS11C.csv FigS11D.csv*: The CSV file
 corresponding to FigS11A FigS11B FigS11C FigS11D. They demonstrated the
 results before and after the density SIRM-restoration of HA-trimer with an
 MC-40 missing wedge (with alignment errors). * *FigS11G.csv FigS11H.csv
 FigS11I.csv FigS11J.csv*: The CSV file corresponding to FigS11A FigS11B
 FigS11C FigS11D. They demonstrated the results before and after the
 density SIRM-restoration of PS-I complex with an MC-40 missing wedge (with
 alignment errors). * *FigS11E.csv FigS11F.csv*: The CSV file corresponding
 to FigS11E FigS11F. They demonstrated the recovery capability of our
 method for Euler angle errors. ### SIRM\_FigS13\_csv.rar * *FigS13A.csv
 FigS13B.csv FigS13C.csv FigS13D.csv FigS13E.csv FigS13F.csv*: The 3D-FSC
 CSV file corresponding to FigS13A FigS13B FigS13C FigS13D FigS13E FigS13F.
 They demonstrated that the recovery effectiveness of SIRM decreases as the
 signal-to-noise ratio (number of particles) decrease. ## Key Information
 Sources ### SIRM\3D-FSC\&Directional-FSC * The 3DFSC and Directional
 FSC calculation software are sourced from
 [https://github.com/LyumkisLab/3DFSC](https://github.com/LyumkisLab/3DFSC). ### SIRM\Figures * The figures are sourced from UCSF Chimera and ChimeraX ### SIRM\Softwares * Softwares are uploaded to [https://github.com/homurachan/SIRM_RELION](https://github.com/homurachan/SIRM_RELION). ## Code/Software ### SIRM\Softwares * Softwares and code are uploaded to [https://github.com/homurachan/SIRM_RELION](https://github.com/homurachan/SIRM_RELION).