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Phycobilisome rod R3 from Gloeobacter violaceus PCC 7421
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
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