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U2 snRNP after ATP-dependent remodelling
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Q3L experimental model PDB 7ABH
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.935 r_dihedral_angle_3_deg 15.484 r_dihedral_angle_4_deg 15.182 r_long_range_B_refined 7.247 r_dihedral_angle_1_deg 6.504 r_angle_refined_deg 1.774 r_mcangle_it 1.619 r_mcbond_it 0.858 r_scbond_it 0.575 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.935 r_dihedral_angle_3_deg 15.484 r_dihedral_angle_4_deg 15.182 r_long_range_B_refined 7.247 r_dihedral_angle_1_deg 6.504 r_angle_refined_deg 1.774 r_mcangle_it 1.619 r_mcbond_it 0.858 r_scbond_it 0.575 r_chiral_restr 0.122 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Remodelled U2 snRNP
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 158286 Reported Resolution (Å) 2.15 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7Q3L, 7Q3L, 7Q3L, 7Q3L, 7Q3L, 7Q3L, 7ABH, 7Q3L) Refinement Space RECIPROCAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 53.45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 0.9 IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING Coot 0.9.4.1 MODEL FITTING UCSF ChimeraX 1.1 MODEL FITTING ISOLDE 1.1 INITIAL EULER ASSIGNMENT cryoSPARC 2.15 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT REFMAC 5 MODEL REFINEMENT LIBG
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1500165