9V7L | pdb_00009v7l

Phycobilisome rod R1 from Gloeobacter violaceus PCC 7421

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.541
r_dihedral_angle_2_deg	16.323
r_dihedral_angle_6_deg	13.613
r_dihedral_angle_1_deg	6.165
r_angle_refined_deg	1.536
r_angle_other_deg	0.525
r_nbd_refined	0.312
r_symmetry_nbd_other	0.222
r_nbtor_refined	0.199
r_xyhbond_nbd_refined	0.183
r_symmetry_xyhbond_nbd_other	0.136
r_ncsr_local_group_70	0.093
r_ncsr_local_group_100	0.093
r_ncsr_local_group_5	0.092
r_ncsr_local_group_11	0.092
r_ncsr_local_group_45	0.092
r_ncsr_local_group_16	0.091
r_ncsr_local_group_51	0.091
r_ncsr_local_group_62	0.091
r_ncsr_local_group_76	0.091
r_ncsr_local_group_130	0.091
r_ncsr_local_group_22	0.09
r_ncsr_local_group_23	0.09
r_ncsr_local_group_91	0.09
r_ncsr_local_group_94	0.09
r_ncsr_local_group_107	0.09
r_ncsr_local_group_77	0.089
r_ncsr_local_group_84	0.089
r_ncsr_local_group_95	0.089
r_ncsr_local_group_97	0.089
r_ncsr_local_group_101	0.089
r_ncsr_local_group_68	0.088
r_ncsr_local_group_90	0.088
r_ncsr_local_group_93	0.088
r_ncsr_local_group_112	0.088
r_ncsr_local_group_128	0.088
r_ncsr_local_group_132	0.088
r_ncsr_local_group_36	0.087
r_ncsr_local_group_42	0.087
r_ncsr_local_group_83	0.087
r_ncsr_local_group_98	0.087
r_ncsr_local_group_120	0.087
r_ncsr_local_group_123	0.087
r_ncsr_local_group_131	0.087
r_ncsr_local_group_2	0.086
r_ncsr_local_group_7	0.086
r_ncsr_local_group_25	0.086
r_ncsr_local_group_29	0.086
r_ncsr_local_group_31	0.086
r_ncsr_local_group_47	0.086
r_ncsr_local_group_99	0.086
r_ncsr_local_group_32	0.085
r_ncsr_local_group_79	0.085
r_ncsr_local_group_115	0.085
r_ncsr_local_group_126	0.085
r_ncsr_local_group_1	0.084
r_ncsr_local_group_24	0.084
r_ncsr_local_group_26	0.084
r_ncsr_local_group_46	0.084
r_ncsr_local_group_54	0.084
r_ncsr_local_group_60	0.084
r_ncsr_local_group_64	0.084
r_ncsr_local_group_27	0.083
r_ncsr_local_group_103	0.083
r_ncsr_local_group_116	0.083
r_ncsr_local_group_4	0.082
r_ncsr_local_group_92	0.082
r_ncsr_local_group_114	0.082
r_ncsr_local_group_30	0.081
r_ncsr_local_group_113	0.081
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_8	0.079
r_ncsr_local_group_10	0.079
r_ncsr_local_group_73	0.078
r_ncsr_local_group_78	0.078
r_ncsr_local_group_124	0.078
r_ncsr_local_group_52	0.077
r_ncsr_local_group_58	0.077
r_ncsr_local_group_104	0.077
r_ncsr_local_group_75	0.076
r_ncsr_local_group_106	0.076
r_ncsr_local_group_129	0.076
r_ncsr_local_group_14	0.075
r_ncsr_local_group_20	0.075
r_ncsr_local_group_43	0.075
r_ncsr_local_group_9	0.074
r_ncsr_local_group_61	0.074
r_ncsr_local_group_67	0.074
r_ncsr_local_group_69	0.074
r_ncsr_local_group_71	0.074
r_ncsr_local_group_81	0.074
r_ncsr_local_group_88	0.074
r_ncsr_local_group_110	0.074
r_ncsr_local_group_127	0.074
r_ncsr_local_group_3	0.073
r_ncsr_local_group_49	0.073
r_ncsr_local_group_44	0.072
r_ncsr_local_group_50	0.072
r_ncsr_local_group_63	0.072
r_ncsr_local_group_105	0.072
r_ncsr_local_group_34	0.07
r_ncsr_local_group_40	0.07
r_ncsr_local_group_65	0.07
r_chiral_restr	0.069
r_ncsr_local_group_72	0.069
r_ncsr_local_group_118	0.069
r_ncsr_local_group_121	0.069
r_ncsr_local_group_80	0.067
r_ncsr_local_group_122	0.067
r_ncsr_local_group_19	0.062
r_ncsr_local_group_13	0.061
r_ncsr_local_group_109	0.061
r_ncsr_local_group_55	0.06
r_ncsr_local_group_12	0.059
r_ncsr_local_group_18	0.059
r_ncsr_local_group_108	0.059
r_ncsr_local_group_37	0.058
r_ncsr_local_group_33	0.057
r_ncsr_local_group_56	0.057
r_ncsr_local_group_39	0.056
r_ncsr_local_group_117	0.056
r_ncsr_local_group_15	0.054
r_ncsr_local_group_21	0.054
r_ncsr_local_group_87	0.053
r_ncsr_local_group_125	0.053
r_ncsr_local_group_53	0.052
r_ncsr_local_group_59	0.052
r_ncsr_local_group_85	0.052
r_ncsr_local_group_111	0.052
r_ncsr_local_group_41	0.048
r_ncsr_local_group_86	0.048
r_ncsr_local_group_119	0.048
r_ncsr_local_group_35	0.047
r_ncsr_local_group_57	0.032
r_ncsr_local_group_48	0.029
r_ncsr_local_group_6	0.028
r_ncsr_local_group_96	0.028
r_ncsr_local_group_28	0.025
r_ncsr_local_group_17	0.015
r_ncsr_local_group_66	0.008
r_gen_planes_refined	0.007
r_ncsr_local_group_82	0.007
r_bond_refined_d	0.006
r_ncsr_local_group_89	0.006
r_ncsr_local_group_38	0.005
r_ncsr_local_group_102	0.005
r_ncsr_local_group_74	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_lrange_it
r_lrange_other

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)	3.76
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