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Crystal structure of proteinase K nanocrystals by electron diffraction with a 20 micrometre C2 condenser aperture
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ID8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.365 α = 90 b = 67.365 β = 90 c = 106.784 γ = 90
Symmetry Space Group P 43 21 2
Data Collection Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.83 83.6 1.275 1.389 0.533 0.498 1.8 10.5
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-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 2ID8 2.701 57.04 6184 297 85.925 0.227 0.2247 0.236 0.2679 0.2816 7.281
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] -0.134 -0.134 0.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.442 r_dihedral_angle_4_deg 19.975 r_dihedral_angle_3_deg 16.12 r_scangle_it 5.536 r_lrange_it 5.499 r_dihedral_angle_1_deg 5.026 r_scbond_it 4.897 r_mcangle_it 3.796 r_mcbond_it 2.992 r_angle_refined_deg 1.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.442 r_dihedral_angle_4_deg 19.975 r_dihedral_angle_3_deg 16.12 r_scangle_it 5.536 r_lrange_it 5.499 r_dihedral_angle_1_deg 5.026 r_scbond_it 4.897 r_mcangle_it 3.796 r_mcbond_it 2.992 r_angle_refined_deg 1.207 r_nbtor_refined 0.315 r_symmetry_xyhbond_nbd_refined 0.216 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.191 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.053 r_metal_ion_refined 0.036 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details Excess liquid was removed by blotting for 4-6s with a Vitrobot
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 67.3653 Length b 67.3653 Length c 67.3653 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (2ID8) Refinement Space RECIPROCAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type OTHER OTHER OTHER OTHER OTHER OTHER OTHER OTHER Electron Dose (electrons/Å**2) 0.034 0.034 0.034 0.034 0.034 0.034 0.034 0.034
Imaging Experiment 1 Date of Experiment 2018-04-20 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
EM Software Task Software Package Version MOLECULAR REPLACEMENT Phaser 2.8.2 SYMMETRY DETERMINATION POINTLESS 1.11.12 CRYSTALLOGRAPHY MERGING AIMLESS 0.7.1 MODEL REFINEMENT REFMAC 5.8.0258
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details