7EFC | pdb_00007efc

1.70 A cryo-EM structure of streptavidin

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N7X
experimental model	PDB	1MK5

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.339
r_lrange_other	24.773
r_lrange_it	24.549
r_dihedral_angle_4_deg	24.548
r_dihedral_angle_3_deg	13.613
r_scangle_it	9.329
r_scangle_other	9.322
r_mcangle_it	8.972
r_mcangle_other	8.966
r_dihedral_angle_1_deg	8.664
r_scbond_it	5.947
r_scbond_other	5.941
r_mcbond_other	5.552
r_mcbond_it	5.546
r_angle_refined_deg	3.022
r_angle_other_deg	2.26
r_ext_dist_refined_d	0.409
r_nbtor_refined	0.099
r_nbd_refined	0.051
r_symmetry_nbd_other	0.049
r_symmetry_nbtor_other	0.038
r_nbd_other	0.035
r_chiral_restr	0.03
r_bond_refined_d	0.027
r_xyhbond_nbd_refined	0.027
r_bond_other_d	0.026
r_symmetry_nbd_refined	0.026
r_symmetry_xyhbond_nbd_refined	0.022
r_gen_planes_refined	0.001
r_gen_planes_other

Sample
Streptavidin

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	153976
Reported Resolution (Å)	1.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	D2

Map-Model Fitting and Refinement
Id	1 (5N7X, 1MK5)
Refinement Space	RECIPROCAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	70

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
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
CTF CORRECTION	CTFFIND	4.1.13
MODEL FITTING	MOLREP
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	REFMAC	5.8.0272

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION