9UPM | pdb_00009upm

Cryo-EM structure of macaque red cone pigment with Q114N mutation

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	23.954
r_lrange_other	23.953
r_dihedral_angle_3_deg	13.841
r_scangle_it	12.532
r_scangle_other	12.529
r_dihedral_angle_2_deg	11.879
r_mcangle_it	10.037
r_mcangle_other	10.033
r_dihedral_angle_6_deg	8.03
r_scbond_it	7.051
r_scbond_other	7.049
r_mcbond_other	5.897
r_mcbond_it	5.895
r_dihedral_angle_1_deg	5.481
r_angle_refined_deg	1.452
r_angle_other_deg	0.623
r_nbd_refined	0.212
r_nbtor_refined	0.182
r_symmetry_nbd_other	0.162
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.066
r_symmetry_xyhbond_nbd_other	0.041
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.001

Sample
MR

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	256022
Reported Resolution (Å)	3.21
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

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

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	46.9

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

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