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Crystal structure of R2-like ligand-binding oxidase from Sulfolobus acidocaldarius solved by 3D micro-crystal electron diffraction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EE4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.31 α = 90 b = 108.93 β = 90 c = 48.17 γ = 90
Symmetry Space Group P 21 21 2
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 28.995 1.35 4423 233 62.52 0.3189 0.3179 0.3326 0.3347 0.3439
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 6.546 f_angle_d 0.411 f_chiral_restr 0.035 f_plane_restr 0.003 f_bond_d 0.002
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building
Sample R2-like ligand-binding oxidase
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) 3 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 63.305 Length b 108.925 Length c 108.925 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (3EE4) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 0.16
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL 2100 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER Nominal Magnification Calibrated Magnification Source LAB6 Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version MODEL FITTING Coot MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE