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Crystal structure of proteinase K lamella by electron diffraction with a 50 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 = 67.331 α = 90 b = 67.331 β = 90 c = 106.878 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 2.06 92.4 1.3 1.45 0.627 0.611 1.8 9.1
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) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 2ID8 2.004 57.034 15759 793 91.825 0.201 0.1991 0.2248 0.2343 0.2467 Random selection 16.43
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] -0.418 -0.418 0.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 16.718 r_dihedral_angle_3_deg 13.967 r_lrange_it 5.677 r_scangle_it 5.529 r_dihedral_angle_1_deg 5.049 r_scbond_it 4.714 r_mcangle_it 3.124 r_mcbond_it 2.646 r_angle_refined_deg 1.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 16.718 r_dihedral_angle_3_deg 13.967 r_lrange_it 5.677 r_scangle_it 5.529 r_dihedral_angle_1_deg 5.049 r_scbond_it 4.714 r_mcangle_it 3.124 r_mcbond_it 2.646 r_angle_refined_deg 1.509 r_nbtor_refined 0.316 r_symmetry_xyhbond_nbd_refined 0.277 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.201 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.054 r_bond_refined_d 0.043 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 67.3308 Length b 67.3308 Length c 67.3308 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 Electron Dose (electrons/Å**2) 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 MODEL REFINEMENT REFMAC 5.8.0258 MOLECULAR REPLACEMENT Phaser 2.8.2 SYMMETRY DETERMINATION POINTLESS 1.11.12 CRYSTALLOGRAPHY MERGING AIMLESS 0.7.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE