9HDR | pdb_00009hdr

Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	26.815
r_long_range_B_other	26.815
r_scangle_other	17.478
r_mcangle_other	15.19
r_mcangle_it	15.189
r_dihedral_angle_3_deg	10.931
r_scbond_it	10.263
r_scbond_other	10.262
r_mcbond_it	9.316
r_mcbond_other	9.311
r_dihedral_angle_1_deg	6.47
r_dihedral_angle_2_deg	5.486
r_angle_refined_deg	1.467
r_angle_other_deg	0.628
r_chiral_restr	0.13
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Sample
Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved
Sample Components
ORF2p
Target DNA

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	121941
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	8000
Maximum Defocus (nm)	22000
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
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	5
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	Coot	0.9.8.92
MODEL FITTING	ISOLDE	1.8
MODEL FITTING	UCSF ChimeraX	1.8
MODEL REFINEMENT	PHENIX	1.21.1-5286
MODEL REFINEMENT	Servalcat	0.4.72
INITIAL EULER ASSIGNMENT	RELION	5
FINAL EULER ASSIGNMENT	RELION	5
CLASSIFICATION	RELION	5
RECONSTRUCTION	RELION	5

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		4568277