5NP7 | pdb_00005np7

CryoEM structure of Human Rad51 on single-stranded DNA to 4.2A resolution.

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	44.967
r_dihedral_angle_2_deg	37.024
r_dihedral_angle_3_deg	23.006
r_mcangle_it	19.492
r_dihedral_angle_4_deg	18.909
r_scbond_it	15.798
r_mcbond_it	11.5
r_dihedral_angle_1_deg	6.724
r_angle_refined_deg	2.647
r_chiral_restr	0.21
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
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
Helical filament of HRAD51 on single-stranded DNA with AMPPNP

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument
Cryogen Name	NITROGEN
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	60000
Reported Resolution (Å)	4.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Helical segments were divided in half, not drawn randomly or odd/even as this would result in some segments from the same filament in both half models. Thus, it is strictly not gold-standard.
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	16
Angular Rotation	56.2

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Maximum likelihood
Overall B Value	94.574
Fitting Procedure
Details	Backbone fitting is good but many of the sidechains cannot be relied on as the map resolution was insufficient.

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2000
Maximum Defocus (nm)
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	59000
Calibrated Magnification	104477
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Ximdisp
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
MODEL FITTING	Coot
CLASSIFICATION	RELION	1.4
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	REFMAC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE	per segment	70000