8AS5

CryoEM structure of the human Nucleophosmin 1 core

ELECTRON MICROSCOPY

---

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
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

Sample
Nucleophosmin 1

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