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Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.77 α = 90 b = 67.4 β = 105.8 c = 73.63 γ = 90
Symmetry Space Group P 1 21 1
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) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 2.4 19.46 1.34 46115 2962 87.76 0.2053 0.2019 0.2267 0.2561 0.2744 Random selection 18.52
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 9.3745 f_angle_d 0.5571 f_chiral_restr 0.0388 f_plane_restr 0.0049 f_bond_d 0.0025
Sample Dye type peroxidase Aa
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details Manual blotting in room temperature with ambient humidity
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 2.4 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 72.77 Length b 67.4 Length c 67.4 Angle Alpha 90 Angle Beta 105.8 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (6I43) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Maximum-likelihood Overall B Value 18.52 Fitting Procedure Details
Data Acquisition Detector Type FEI CETA (4k x 4k) Electron Dose (electrons/Å**2) 0.115
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 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 PHENIX MOLECULAR REPLACEMENT PHENIX CRYSTALLOGRAPHY MERGING PHENIX RECONSTRUCTION PHENIX MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE