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Electron crystallographic structure of Catalase using a direct electron detector at 300 kV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.98 α = 90 b = 174.02 β = 90 c = 199.45 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 electron 2020-08-26 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 0.0197
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 3 131.126 82.3 1.159 1.173 0.688 3.79 43.552 40941 8.65
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 3.18 82.7 1.786 1.808 0.185 1.9 42.194
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 THROUGHOUT 3.2 131.126 1.35 33768 1651 82.15 0.3109 0.3089 0.3139 0.3482 0.3511 16.7903
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 15.158 f_angle_d 0.731 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 588
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction
Specimen Preparation Sample Aggregation State TISSUE
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 70 Length b 174.2 Length c 174.2 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type DIRECT ELECTRON DE-64 (8k x 8k) Electron Dose (electrons/Å**2) 0.0025
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 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) 300 Imaging Details
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE