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Catalase structure determined by eEFD (dataset 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NWL
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.109 α = 90 b = 171.901 β = 90 c = 195.013 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 2018-09-26
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 47.35 1.6 38238 1984 82.6 0.2526 0.2508 0.264 0.283 0.2917
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 11.173 f_angle_d 0.65 f_chiral_restr 0.043 f_bond_d 0.006 f_plane_restr 0.004
Software Software Software Name Purpose PHENIX refinement
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name NITROGEN 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 69.1 Length b 171.9 Length c 171.9 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (3NWL) Refinement Space RECIPROCAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 2.9
Imaging Experiment 1 Date of Experiment 2018-09-26 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 OTHER Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL REFINEMENT PHENIX 1.14_3260
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE