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In situ MicroED structure of human eosinophil major basic protein-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H8U in silico model AlphaFold AF-P13727-F1-model_v4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.7 α = 90 b = 57.9 β = 91.1 c = 58.2 γ = 90
Symmetry Space Group P 1 21 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 99.4 0.571 0.582 0.82 5.68 7771 47.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.44 98.4 1.637 1.684 0.611
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY FREE R-VALUE 3 19.89 1.34 4282 433 98.03 0.2593 0.253 0.2669 0.3127 0.3295 40.48
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.4532 f_angle_d 0.6242 f_chiral_restr 0.0467 f_plane_restr 0.0089 f_bond_d 0.0029
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHENIX phasing
Sample In situ MicroED structure of the human eosinophil major basic protein-1
Specimen Preparation Sample Aggregation State CELL Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 3 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 30.7 Length b 57.9 Length c 57.9 Angle Alpha 90 Angle Beta 91.1 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (1h8u) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Iterative refinement in phenix.refine and modeling building in coot
Data Acquisition Detector Type FEI CETA (4k x 4k) Electron Dose (electrons/Å**2) 0.1
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS 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 FITTING Coot 0.9.8.92 MOLECULAR REPLACEMENT PHENIX 1.21.1-5286 RECONSTRUCTION PHENIX 1.21.1-5286 MODEL REFINEMENT PHENIX 1.21.1_5286
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE