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.
CryoEM structure of the human Polycystin-2/PKD2 TRP channel
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
30.759
r_dihedral_angle_4_deg
15.678
r_dihedral_angle_3_deg
13.272
r_long_range_B_refined
12.001
r_long_range_B_other
12
r_mcangle_other
7.749
r_mcangle_it
7.748
r_scangle_other
6.486
r_dihedral_angle_1_deg
5.875
r_mcbond_it
4.266
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
30.759
r_dihedral_angle_4_deg
15.678
r_dihedral_angle_3_deg
13.272
r_long_range_B_refined
12.001
r_long_range_B_other
12
r_mcangle_other
7.749
r_mcangle_it
7.748
r_scangle_other
6.486
r_dihedral_angle_1_deg
5.875
r_mcbond_it
4.266
r_mcbond_other
4.263
r_scbond_it
3.422
r_scbond_other
3.422
r_angle_refined_deg
1.037
r_angle_other_deg
0.848
r_chiral_restr
0.053
r_bond_refined_d
0.007
r_gen_planes_refined
0.003
r_bond_other_d
0.001
r_gen_planes_other
0.001
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
Polycystin-2 channel tetramer
(residues 185-723)
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3 microlitres were applied to the grid and blotted for 3secs prior to plunge in liquid ethane
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
19546
Reported Resolution (Å)
4.22
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Resolution determined by gold-standard FSC procedure as implemented in RELION
Refinement Type
Symmetry Type
POINT
Point Symmetry
C4
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Model was built directly into map de novo
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
45.1
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI POLARA 300
Minimum Defocus (nm)
1100
Maximum Defocus (nm)
4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
SIDE ENTRY, EUCENTRIC
Nominal Magnification
37037
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
1.3
IMAGE ACQUISITION
SerialEM
CTF CORRECTION
CTFFIND
4.0.8
CTF CORRECTION
RELION
1.3
MODEL FITTING
Coot
MODEL REFINEMENT
REFMAC
5.8.0135
INITIAL EULER ASSIGNMENT
RELION
1.3
FINAL EULER ASSIGNMENT
RELION
1.3
CLASSIFICATION
RELION
1.3
RECONSTRUCTION
RELION
1.3
MODEL REFINEMENT
RELION
1.3
MODEL REFINEMENT
CTFFIND
4
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF correction as implemented in CTTFIND4/RELION
161965
Particles were autopicked using CTF-corrected template based picking algorithm in RELION using selected 2D class averages based on manually picked particles.