9V7I | pdb_00009v7i

Phycobilisome rod R3 from Gloeobacter violaceus PCC 7421

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.249
r_dihedral_angle_2_deg	16.278
r_dihedral_angle_6_deg	13.904
r_dihedral_angle_1_deg	6.18
r_lrange_it	4.351
r_lrange_other	4.351
r_mcangle_it	2.428
r_mcangle_other	2.428
r_scangle_it	2.428
r_scangle_other	2.428
r_angle_refined_deg	1.645
r_mcbond_it	1.409
r_mcbond_other	1.409
r_scbond_it	1.33
r_scbond_other	1.33
r_angle_other_deg	0.636
r_nbd_refined	0.312
r_symmetry_nbd_other	0.223
r_nbtor_refined	0.204
r_xyhbond_nbd_refined	0.173
r_ncsr_local_group_27	0.118
r_ncsr_local_group_25	0.112
r_ncsr_local_group_26	0.112
r_ncsr_local_group_31	0.112
r_ncsr_local_group_107	0.111
r_ncsr_local_group_1	0.109
r_ncsr_local_group_32	0.109
r_ncsr_local_group_24	0.106
r_ncsr_local_group_91	0.106
r_ncsr_local_group_23	0.105
r_ncsr_local_group_30	0.105
r_ncsr_local_group_29	0.104
r_ncsr_local_group_77	0.102
r_ncsr_local_group_95	0.102
r_ncsr_local_group_11	0.101
r_ncsr_local_group_68	0.101
r_ncsr_local_group_93	0.101
r_ncsr_local_group_5	0.1
r_ncsr_local_group_62	0.1
r_ncsr_local_group_123	0.1
r_ncsr_local_group_128	0.1
r_symmetry_xyhbond_nbd_other	0.099
r_ncsr_local_group_45	0.099
r_ncsr_local_group_51	0.099
r_ncsr_local_group_83	0.099
r_ncsr_local_group_94	0.099
r_ncsr_local_group_97	0.099
r_ncsr_local_group_112	0.099
r_ncsr_local_group_130	0.099
r_ncsr_local_group_131	0.099
r_ncsr_local_group_100	0.098
r_ncsr_local_group_71	0.096
r_ncsr_local_group_70	0.095
r_ncsr_local_group_76	0.095
r_ncsr_local_group_92	0.094
r_ncsr_local_group_88	0.093
r_ncsr_local_group_103	0.093
r_ncsr_local_group_116	0.092
r_ncsr_local_group_16	0.091
r_ncsr_local_group_84	0.091
r_ncsr_local_group_90	0.091
r_ncsr_local_group_22	0.09
r_ncsr_local_group_58	0.09
r_ncsr_local_group_69	0.09
r_ncsr_local_group_79	0.089
r_ncsr_local_group_115	0.089
r_ncsr_local_group_124	0.089
r_ncsr_local_group_52	0.088
r_ncsr_local_group_78	0.088
r_ncsr_local_group_104	0.088
r_ncsr_local_group_20	0.087
r_ncsr_local_group_46	0.087
r_ncsr_local_group_54	0.087
r_ncsr_local_group_60	0.087
r_ncsr_local_group_101	0.087
r_ncsr_local_group_106	0.087
r_ncsr_local_group_132	0.087
r_ncsr_local_group_42	0.086
r_ncsr_local_group_99	0.086
r_ncsr_local_group_36	0.085
r_ncsr_local_group_73	0.085
r_ncsr_local_group_126	0.085
r_ncsr_local_group_129	0.085
r_ncsr_local_group_98	0.084
r_ncsr_local_group_120	0.084
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_7	0.083
r_ncsr_local_group_14	0.083
r_ncsr_local_group_40	0.083
r_ncsr_local_group_75	0.083
r_ncsr_local_group_110	0.083
r_ncsr_local_group_55	0.082
r_ncsr_local_group_64	0.082
r_ncsr_local_group_114	0.082
r_ncsr_local_group_8	0.081
r_ncsr_local_group_28	0.081
r_ncsr_local_group_113	0.081
r_ncsr_local_group_118	0.081
r_ncsr_local_group_4	0.08
r_ncsr_local_group_10	0.08
r_ncsr_local_group_47	0.08
r_ncsr_local_group_109	0.08
r_ncsr_local_group_2	0.079
r_ncsr_local_group_63	0.079
r_ncsr_local_group_105	0.079
r_ncsr_local_group_34	0.078
r_ncsr_local_group_37	0.078
r_ncsr_local_group_108	0.078
r_ncsr_local_group_72	0.077
r_ncsr_local_group_61	0.076
r_ncsr_local_group_81	0.076
r_ncsr_local_group_65	0.075
r_ncsr_local_group_67	0.075
r_ncsr_local_group_121	0.075
r_ncsr_local_group_127	0.075
r_ncsr_local_group_80	0.074
r_ncsr_local_group_111	0.074
r_ncsr_local_group_122	0.074
r_ncsr_local_group_43	0.073
r_ncsr_local_group_49	0.072
r_ncsr_local_group_3	0.071
r_ncsr_local_group_9	0.071
r_ncsr_local_group_96	0.07
r_chiral_restr	0.069
r_ncsr_local_group_15	0.069
r_ncsr_local_group_50	0.069
r_ncsr_local_group_44	0.068
r_ncsr_local_group_53	0.067
r_ncsr_local_group_13	0.066
r_ncsr_local_group_33	0.064
r_ncsr_local_group_87	0.064
r_ncsr_local_group_12	0.063
r_ncsr_local_group_19	0.063
r_ncsr_local_group_85	0.063
r_ncsr_local_group_18	0.062
r_ncsr_local_group_56	0.062
r_ncsr_local_group_17	0.061
r_ncsr_local_group_35	0.06
r_ncsr_local_group_39	0.06
r_ncsr_local_group_86	0.06
r_ncsr_local_group_117	0.059
r_ncsr_local_group_21	0.058
r_ncsr_local_group_59	0.056
r_ncsr_local_group_125	0.054
r_ncsr_local_group_41	0.052
r_ncsr_local_group_74	0.052
r_ncsr_local_group_119	0.052
r_ncsr_local_group_6	0.047
r_ncsr_local_group_89	0.04
r_ncsr_local_group_57	0.031
r_ncsr_local_group_48	0.029
r_ncsr_local_group_102	0.02
r_ncsr_local_group_38	0.012
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_ncsr_local_group_66	0.006
r_ncsr_local_group_82	0.006
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)	3.03
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