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Protein structure determination by electron diffraction using a single three-dimensional nanocrystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YBL
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.56 α = 90 b = 68.05 β = 90 c = 32.05 γ = 90
Symmetry Space Group P 21 21 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT NONE 2ybl 2.11 41.46 6717 6717 48.38 0.335 0.3472 0.35 23.986
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.058 r_dihedral_angle_3_deg 19.255 r_dihedral_angle_4_deg 16.435 r_dihedral_angle_1_deg 6.563 r_angle_refined_deg 1.784 r_long_range_B_refined 1.563 r_long_range_B_other 1.563 r_angle_other_deg 1.208 r_scangle_other 1.01 r_mcangle_it 1.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.058 r_dihedral_angle_3_deg 19.255 r_dihedral_angle_4_deg 16.435 r_dihedral_angle_1_deg 6.563 r_angle_refined_deg 1.784 r_long_range_B_refined 1.563 r_long_range_B_other 1.563 r_angle_other_deg 1.208 r_scangle_other 1.01 r_mcangle_it 1.008 r_mcangle_other 1.008 r_mcbond_it 0.749 r_mcbond_other 0.748 r_scbond_it 0.748 r_scbond_other 0.747 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Software Software Software Name Purpose REFMAC refinement
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 104.56 Length b 68.05 Length c 68.05 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 0.01
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE