☰ Navigation Tabs
Catalase structure determined by electron crystallography of thin 3D crystals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69 α = 90 b = 173.5 β = 90 c = 206 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
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3NWL 3.2 19.988 1.81 30337 844 73.01 0.252 0.2505 0.2668 0.3043 0.2888
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 13.406 f_angle_d 0.885 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.006
Software Software Software Name Purpose PHENIX refinement EDINT data scaling Modified version of phenix phasing Modified phasing
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) Resolution Method Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 69 Length b 173.5 Length c 173.5 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TVIPS TEMCAM-F224 (2k x 2k) Electron Dose (electrons/Å**2) 0.01
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model HITACHI EF3000 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE