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Ab initio structure of proteinase K from electron-counted MicroED data
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.08 α = 90 b = 67.08 β = 90 c = 106.78 γ = 90
Symmetry Space Group P 43 21 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY FREE R-VALUE 1.5 43.386 39303 2001 98.848 0.152 0.1495 0.2046 Random 14.137
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] -0.47 -0.47 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.941 r_dihedral_angle_4_deg 21.837 r_dihedral_angle_3_deg 12.286 r_dihedral_angle_1_deg 6.758 r_lrange_it 5.137 r_lrange_other 4.919 r_scangle_it 4.493 r_scangle_other 4.491 r_scbond_it 3.624 r_scbond_other 3.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.941 r_dihedral_angle_4_deg 21.837 r_dihedral_angle_3_deg 12.286 r_dihedral_angle_1_deg 6.758 r_lrange_it 5.137 r_lrange_other 4.919 r_scangle_it 4.493 r_scangle_other 4.491 r_scbond_it 3.624 r_scbond_other 3.589 r_rigid_bond_restr 2.679 r_mcangle_it 2.35 r_mcangle_other 2.35 r_mcbond_it 1.877 r_mcbond_other 1.858 r_angle_other_deg 1.721 r_angle_refined_deg 1.691 r_symmetry_xyhbond_nbd_refined 0.405 r_symmetry_nbd_refined 0.333 r_nbd_other 0.239 r_nbd_refined 0.221 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_other 0.127 r_symmetry_xyhbond_nbd_other 0.098 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.083 r_metal_ion_refined 0.039 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2029 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument LEICA PLUNGER 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 67.08 Length b 67.08 Length c 67.08 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol AB INITIO MODEL Refinement Target Maximum likelihood Overall B Value 14.137 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 0.001
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode DIFFRACTION Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL REFINEMENT REFMAC CRYSTALLOGRAPHY MERGING AIMLESS RECONSTRUCTION REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE