9V7G | pdb_00009v7g

Phycobilisome Rx rod from Gloeobacter violaceus PCC 7421

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.139
r_dihedral_angle_3_deg	17.008
r_dihedral_angle_6_deg	15.188
r_lrange_it	5.671
r_lrange_other	5.671
r_dihedral_angle_1_deg	4.844
r_scangle_it	4.283
r_scangle_other	4.283
r_mcangle_it	3.391
r_mcangle_other	3.391
r_scbond_it	2.502
r_scbond_other	2.502
r_mcbond_it	2.164
r_mcbond_other	2.164
r_angle_refined_deg	1.581
r_angle_other_deg	0.661
r_nbd_refined	0.219
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.167
r_ncsr_local_group_22	0.112
r_ncsr_local_group_7	0.111
r_ncsr_local_group_8	0.109
r_ncsr_local_group_27	0.108
r_ncsr_local_group_23	0.103
r_ncsr_local_group_15	0.102
r_ncsr_local_group_16	0.102
r_ncsr_local_group_28	0.102
r_ncsr_local_group_9	0.101
r_ncsr_local_group_10	0.1
r_ncsr_local_group_24	0.099
r_ncsr_local_group_17	0.098
r_chiral_restr	0.097
r_ncsr_local_group_2	0.096
r_ncsr_local_group_18	0.096
r_ncsr_local_group_4	0.091
r_ncsr_local_group_6	0.089
r_ncsr_local_group_11	0.089
r_ncsr_local_group_13	0.088
r_ncsr_local_group_21	0.088
r_ncsr_local_group_30	0.088
r_ncsr_local_group_3	0.087
r_ncsr_local_group_29	0.087
r_ncsr_local_group_1	0.084
r_ncsr_local_group_14	0.084
r_ncsr_local_group_20	0.083
r_ncsr_local_group_26	0.082
r_ncsr_local_group_5	0.081
r_ncsr_local_group_12	0.079
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_19	0.077
r_ncsr_local_group_25	0.075
r_symmetry_xyhbond_nbd_other	0.061
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001

Sample
Bundle-shaped phycobilisome

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	746972
Reported Resolution (Å)	2.72
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)	66

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	0.01
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	85000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Preliminary grid screening was performed manually.

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM	4.04
CTF CORRECTION	Warp	1.0.9
FINAL EULER ASSIGNMENT	cryoSPARC	4.7
RECONSTRUCTION	cryoSPARC	4.7

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