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In situ microED structure of the 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 = 31.24 α = 90 b = 57.87 β = 90 c = 59.06 γ = 90
Symmetry Space Group P 2 21 21
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 3.2 96.1 0.69 0.719 0.931 3.2 1912 85.01
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 3.2 3.29 98 4.13 4.29 0.559
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY FREE R-VALUE 3.2 28.93 1882 199 95.58 0.2727 0.2679 0.2858 0.311 0.3431 Random selection 91.79
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 12.6272 f_angle_d 1.0433 f_chiral_restr 0.0573 f_plane_restr 0.007 f_bond_d 0.0055
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction XSCALE data scaling
Sample In situ microED structure of the Eosinophil major basic protein-1
Specimen Preparation Sample Aggregation State CELL Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Blot time of 6~8 sec, single-side back blotting
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 3.2 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 31.24 Length b 57.87 Length c 57.87 Angle Alpha 90 Angle Beta 90 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 Alternating rounds of phenix.refine and map filling in Coot
Data Acquisition Detector Type FEI CETA (4k x 4k) Electron Dose (electrons/Å**2) 0.15
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 IMAGE ACQUISITION EPU 1.13 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