9V7H | pdb_00009v7h

Phycobilisome rod R2 from Gloeobacter violaceus PCC 7421

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.86
r_dihedral_angle_2_deg	15.698
r_dihedral_angle_6_deg	13.903
r_dihedral_angle_1_deg	6.148
r_lrange_it	4.476
r_lrange_other	4.476
r_scangle_it	2.758
r_scangle_other	2.758
r_mcangle_it	2.514
r_mcangle_other	2.514
r_angle_refined_deg	1.737
r_scbond_it	1.54
r_scbond_other	1.54
r_mcbond_it	1.516
r_mcbond_other	1.516
r_angle_other_deg	0.666
r_nbd_refined	0.318
r_symmetry_nbd_other	0.223
r_nbtor_refined	0.208
r_xyhbond_nbd_refined	0.178
r_symmetry_xyhbond_nbd_other	0.152
r_ncsr_local_group_91	0.105
r_ncsr_local_group_5	0.104
r_ncsr_local_group_107	0.104
r_ncsr_local_group_26	0.103
r_ncsr_local_group_27	0.102
r_ncsr_local_group_62	0.102
r_ncsr_local_group_94	0.102
r_ncsr_local_group_77	0.101
r_ncsr_local_group_93	0.101
r_ncsr_local_group_95	0.101
r_ncsr_local_group_45	0.1
r_ncsr_local_group_11	0.099
r_ncsr_local_group_32	0.097
r_ncsr_local_group_68	0.097
r_ncsr_local_group_1	0.096
r_ncsr_local_group_31	0.096
r_ncsr_local_group_25	0.095
r_ncsr_local_group_128	0.095
r_ncsr_local_group_51	0.094
r_ncsr_local_group_92	0.094
r_ncsr_local_group_131	0.094
r_ncsr_local_group_83	0.093
r_ncsr_local_group_103	0.093
r_ncsr_local_group_123	0.093
r_ncsr_local_group_23	0.092
r_ncsr_local_group_29	0.092
r_ncsr_local_group_24	0.09
r_ncsr_local_group_30	0.09
r_ncsr_local_group_70	0.089
r_ncsr_local_group_76	0.089
r_ncsr_local_group_115	0.089
r_ncsr_local_group_16	0.088
r_ncsr_local_group_22	0.088
r_ncsr_local_group_79	0.088
r_ncsr_local_group_100	0.088
r_ncsr_local_group_106	0.088
r_ncsr_local_group_130	0.088
r_ncsr_local_group_46	0.087
r_ncsr_local_group_78	0.087
r_ncsr_local_group_97	0.087
r_ncsr_local_group_112	0.087
r_ncsr_local_group_7	0.086
r_ncsr_local_group_104	0.086
r_ncsr_local_group_116	0.086
r_symmetry_nbtor_other	0.084
r_ncsr_local_group_42	0.084
r_ncsr_local_group_54	0.084
r_ncsr_local_group_60	0.084
r_ncsr_local_group_98	0.084
r_ncsr_local_group_10	0.083
r_ncsr_local_group_36	0.083
r_ncsr_local_group_64	0.083
r_ncsr_local_group_84	0.083
r_ncsr_local_group_90	0.083
r_ncsr_local_group_99	0.083
r_ncsr_local_group_101	0.083
r_ncsr_local_group_114	0.083
r_ncsr_local_group_120	0.083
r_ncsr_local_group_126	0.083
r_ncsr_local_group_132	0.083
r_ncsr_local_group_2	0.082
r_ncsr_local_group_4	0.082
r_ncsr_local_group_47	0.082
r_ncsr_local_group_113	0.082
r_ncsr_local_group_8	0.08
r_ncsr_local_group_63	0.079
r_ncsr_local_group_105	0.079
r_ncsr_local_group_52	0.077
r_ncsr_local_group_58	0.077
r_ncsr_local_group_67	0.077
r_ncsr_local_group_73	0.077
r_ncsr_local_group_81	0.077
r_ncsr_local_group_124	0.077
r_ncsr_local_group_127	0.077
r_ncsr_local_group_61	0.076
r_ncsr_local_group_14	0.075
r_ncsr_local_group_71	0.075
r_ncsr_local_group_20	0.074
r_ncsr_local_group_75	0.074
r_ncsr_local_group_110	0.074
r_ncsr_local_group_3	0.073
r_ncsr_local_group_9	0.073
r_ncsr_local_group_43	0.073
r_ncsr_local_group_49	0.073
r_ncsr_local_group_65	0.073
r_ncsr_local_group_69	0.073
r_ncsr_local_group_88	0.073
r_ncsr_local_group_121	0.073
r_ncsr_local_group_129	0.073
r_ncsr_local_group_72	0.072
r_ncsr_local_group_118	0.071
r_chiral_restr	0.07
r_ncsr_local_group_34	0.07
r_ncsr_local_group_40	0.07
r_ncsr_local_group_50	0.07
r_ncsr_local_group_44	0.069
r_ncsr_local_group_80	0.068
r_ncsr_local_group_122	0.068
r_ncsr_local_group_55	0.059
r_ncsr_local_group_109	0.059
r_ncsr_local_group_13	0.058
r_ncsr_local_group_18	0.058
r_ncsr_local_group_19	0.058
r_ncsr_local_group_37	0.058
r_ncsr_local_group_96	0.058
r_ncsr_local_group_108	0.058
r_ncsr_local_group_12	0.057
r_ncsr_local_group_117	0.056
r_ncsr_local_group_39	0.055
r_ncsr_local_group_56	0.055
r_ncsr_local_group_33	0.054
r_ncsr_local_group_28	0.053
r_ncsr_local_group_85	0.053
r_ncsr_local_group_111	0.053
r_ncsr_local_group_15	0.052
r_ncsr_local_group_21	0.052
r_ncsr_local_group_59	0.048
r_ncsr_local_group_41	0.047
r_ncsr_local_group_53	0.047
r_ncsr_local_group_86	0.047
r_ncsr_local_group_87	0.047
r_ncsr_local_group_119	0.047
r_ncsr_local_group_125	0.047
r_ncsr_local_group_35	0.046
r_ncsr_local_group_6	0.045
r_ncsr_local_group_48	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_ncsr_local_group_74	0.007
r_ncsr_local_group_102	0.007
r_ncsr_local_group_17	0.006
r_ncsr_local_group_57	0.006
r_ncsr_local_group_66	0.006
r_ncsr_local_group_82	0.006
r_ncsr_local_group_89	0.006
r_ncsr_local_group_38	0.005
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	207644
Reported Resolution (Å)	2.95
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