☰ Navigation Tabs
CryoEM structure of the human Nucleophosmin 1 core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EHD
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.246 r_lrange_other 30.245 r_mcangle_it 18.314 r_mcangle_other 18.311 r_scangle_it 16.797 r_scangle_other 16.794 r_dihedral_angle_3_deg 16.504 r_dihedral_angle_6_deg 14.099 r_mcbond_it 11.415 r_mcbond_other 11.415
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.246 r_lrange_other 30.245 r_mcangle_it 18.314 r_mcangle_other 18.311 r_scangle_it 16.797 r_scangle_other 16.794 r_dihedral_angle_3_deg 16.504 r_dihedral_angle_6_deg 14.099 r_mcbond_it 11.415 r_mcbond_other 11.415 r_scbond_it 9.396 r_scbond_other 9.393 r_dihedral_angle_2_deg 4.781 r_dihedral_angle_1_deg 4.721 r_angle_refined_deg 1.045 r_angle_other_deg 0.32 r_ncsr_local_group_2 0.238 r_ncsr_local_group_6 0.234 r_ncsr_local_group_7 0.228 r_ncsr_local_group_3 0.226 r_ncsr_local_group_10 0.224 r_ncsr_local_group_1 0.221 r_ncsr_local_group_5 0.221 r_ncsr_local_group_8 0.219 r_ncsr_local_group_4 0.216 r_ncsr_local_group_9 0.212 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.173 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.053 r_chiral_restr 0.046 r_chiral_restr_other 0.026 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.001 r_bond_other_d
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 106905 Reported Resolution (Å) 3.53 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5EHD) Refinement Space RECIPROCAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 54
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU MODEL FITTING Coot 0.9.8.1 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT RELION MODEL REFINEMENT REFMAC 5.8.0352
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION