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Cryo-EM structure of native Rubisco from Nitrosospira multiformis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F0H
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.654 r_lrange_other 24.654 r_scangle_it 18.529 r_scangle_other 18.529 r_dihedral_angle_3_deg 16.32 r_mcangle_other 15.883 r_mcangle_it 15.882 r_dihedral_angle_6_deg 15.087 r_scbond_it 12.659 r_scbond_other 12.659
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.654 r_lrange_other 24.654 r_scangle_it 18.529 r_scangle_other 18.529 r_dihedral_angle_3_deg 16.32 r_mcangle_other 15.883 r_mcangle_it 15.882 r_dihedral_angle_6_deg 15.087 r_scbond_it 12.659 r_scbond_other 12.659 r_mcbond_it 11.331 r_mcbond_other 11.33 r_dihedral_angle_1_deg 7.088 r_dihedral_angle_2_deg 6.941 r_angle_refined_deg 1.919 r_angle_other_deg 0.625 r_xyhbond_nbd_refined 0.231 r_nbd_refined 0.22 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.189 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_1 0.081 r_ncsr_local_group_12 0.079 r_ncsr_local_group_8 0.077 r_ncsr_local_group_5 0.076 r_ncsr_local_group_7 0.076 r_ncsr_local_group_10 0.076 r_ncsr_local_group_2 0.075 r_ncsr_local_group_3 0.074 r_ncsr_local_group_4 0.074 r_ncsr_local_group_26 0.074 r_ncsr_local_group_6 0.072 r_ncsr_local_group_16 0.071 r_ncsr_local_group_21 0.071 r_ncsr_local_group_23 0.07 r_ncsr_local_group_14 0.069 r_ncsr_local_group_25 0.069 r_ncsr_local_group_28 0.069 r_ncsr_local_group_19 0.068 r_ncsr_local_group_18 0.067 r_ncsr_local_group_13 0.056 r_ncsr_local_group_9 0.048 r_ncsr_local_group_11 0.045 r_ncsr_local_group_24 0.044 r_ncsr_local_group_15 0.043 r_ncsr_local_group_27 0.043 r_ncsr_local_group_49 0.042 r_ncsr_local_group_38 0.041 r_ncsr_local_group_39 0.04 r_ncsr_local_group_40 0.04 r_ncsr_local_group_29 0.039 r_ncsr_local_group_50 0.038 r_ncsr_local_group_48 0.037 r_ncsr_local_group_17 0.036 r_ncsr_local_group_33 0.036 r_ncsr_local_group_37 0.036 r_ncsr_local_group_22 0.035 r_ncsr_local_group_45 0.035 r_ncsr_local_group_35 0.034 r_ncsr_local_group_41 0.034 r_ncsr_local_group_51 0.034 r_ncsr_local_group_52 0.034 r_ncsr_local_group_53 0.033 r_ncsr_local_group_30 0.032 r_ncsr_local_group_31 0.032 r_ncsr_local_group_43 0.032 r_ncsr_local_group_47 0.032 r_ncsr_local_group_34 0.031 r_ncsr_local_group_56 0.031 r_ncsr_local_group_20 0.03 r_ncsr_local_group_54 0.03 r_ncsr_local_group_32 0.029 r_ncsr_local_group_44 0.029 r_ncsr_local_group_36 0.027 r_ncsr_local_group_42 0.027 r_ncsr_local_group_46 0.027 r_symmetry_xyhbond_nbd_other 0.023 r_ncsr_local_group_55 0.023 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.001 r_bond_other_d
Sample Ribulose bisphosphate carboxylase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 64288 Reported Resolution (Å) 2.26 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D4
Map-Model Fitting and Refinement Id 1 (4F0H) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 600 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model JEOL Nominal Magnification 57000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 5.0.1 IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING Coot 0.9.8 INITIAL EULER ASSIGNMENT RELION 5.0.1 FINAL EULER ASSIGNMENT RELION 5.0.1 CLASSIFICATION RELION 5.0.1 RECONSTRUCTION RELION 5.0.1 MODEL REFINEMENT Servalcat 0.4.131
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1577431 Perform 2D sorting on the particles collected via LoG picking, train Topaz on the useful ones, and then perform Topaz picking