Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Cryo-EM structure of the light-driven sodium-pumping rhodopsin KR2
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_3_deg
14.413
r_long_range_B_refined
10.211
r_long_range_B_other
10.211
r_scangle_other
8.715
r_dihedral_angle_2_deg
8.53
r_mcangle_it
5.686
r_mcangle_other
5.686
r_scbond_it
5.644
r_scbond_other
5.644
r_dihedral_angle_1_deg
5.028
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_3_deg
14.413
r_long_range_B_refined
10.211
r_long_range_B_other
10.211
r_scangle_other
8.715
r_dihedral_angle_2_deg
8.53
r_mcangle_it
5.686
r_mcangle_other
5.686
r_scbond_it
5.644
r_scbond_other
5.644
r_dihedral_angle_1_deg
5.028
r_mcbond_it
3.942
r_mcbond_other
3.937
r_angle_refined_deg
1.427
r_angle_other_deg
0.472
r_chiral_restr
0.083
r_bond_refined_d
0.01
r_gen_planes_refined
0.008
r_gen_planes_other
0.001
r_bond_other_d
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
Sodium-pumping rhodopsin
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
Cryogen Name
ETHANE
Sample Vitrification Details
Jet vitrified with EasyGrid
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
333078
Reported Resolution (Å)
2.32
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C5
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
40.3
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2400
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
105000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.2
IMAGE ACQUISITION
EPU
CTF CORRECTION
cryoSPARC
4.2
INITIAL EULER ASSIGNMENT
cryoSPARC
4.2
FINAL EULER ASSIGNMENT
cryoSPARC
4.2
CLASSIFICATION
cryoSPARC
4.2
RECONSTRUCTION
cryoSPARC
4.2
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
1916000
A first round of blob picking was performed and used to obtain an initial model. this initial model was used to generate templates that were then used to performed template picking, resulting in 1916000 particles