2023-07-12 REL PDBe PDBe PDBe 2022-07-01 2023-07-12 2023-07-12 2023-07-12 Czech Science Foundation GA22-19896S Czech Republic Ministry of Education, Youth and Sports of the Czech Republic LM2018127 Czech Republic Mouse endoribonuclease Dicer Zanova M Zapletal D Kubicek K Stefl R Pinkas M Novacek J endoribonuclease, gene silencing, post-transcriptional, catalytic enzyme, cytoplasm, RNA BINDING PROTEIN Zapletal D Kubicek K Zanova M Sebesta M Pinkas M Malik R Joseph DF Novacek J Svoboda P Stefl R Mammalian Dicer uses its helicase domain to control RNA processing To Be Published 0353 EMD-15299 associated EM volume Free form of mouse somatic dicer Free form of mouse somatic dicer 0 1 Mus musculus singleParticle particle 0.20 8.0 50.0 Tris 100.0 Sodium Chloride 1.0 Dithiotreitol 2.0 Magensium Chloride
The buffer was always prepared fresh
 ETHANE 100 277.15 FEI VITROBOT MARK IV
Described in STAR methods.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 3.5 GATAN K2 SUMMIT (4k x 4k) COUNTING 6354 55.0 1 862842 81 FOURIER SPACE 4.18 FSC 0.143 CUT-OFF cryoSPARC v3.3.1
Locally refined electron density map of Dicer helicase domain
92906 NOT APPLICABLE NOT APPLICABLE 100 1377.0 cryoSPARC v3.3.1 emd_15299.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.14186405 3.9037466 0.000424258 0.014920531 0.828 0.828 0.828 0.0991 AUTHOR Locally refined electron density map of Dicer helicase domain FLEXIBLE FIT
Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting into combined map from locally refined protein parts was done using Chimera and then Coot's Real Space Refine Zone.
Ramachandran Plot, Rotamer Analysis, Density Analysis REAL 87.799999999999997 FLEXIBLE FIT
PHENIX Real-space refinement was used for flexible fitting.
Correlation coefficient REAL 87.799999999999997 FLEXIBLE FIT
ISOLDE was used for flexible fitting with defined torsion restraints
Ramachandran Plot, Rotamer Analysis, Clash Score REAL 87.799999999999997 emd_15299_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.41366518 1.4321444 0.00023302798 0.020253109 0.828 0.828 0.828 AUTHOR half map A emd_15299_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 317.952 317.952 317.952 90.0 90.0 90.0 X Y Z -0.3771957 1.3784842 0.00023050126 0.020312319 0.828 0.828 0.828 AUTHOR half map B