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3D electron diffraction structure of thaumatin from Thaumatococcus daniellii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C5Y
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.72 α = 90 b = 57.72 β = 90 c = 149.17 γ = 90
Symmetry Space Group P 41 21 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 6C5Y 2.76 45.69 4364 231 65.61 0.2822 0.2801 0.2859 0.321 0.3195 RANDOM 31.346
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] -0.03 -0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_3_deg 19.814 r_dihedral_angle_4_deg 17.613 r_dihedral_angle_1_deg 8.394 r_angle_refined_deg 1.009 r_angle_other_deg 0.753 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_3_deg 19.814 r_dihedral_angle_4_deg 17.613 r_dihedral_angle_1_deg 8.394 r_angle_refined_deg 1.009 r_angle_other_deg 0.753 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASER 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 DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 57.72 Length b 57.72 Length c 57.72 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 Structure refined with REFMAC against diffraction data
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA 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) 200 Imaging Details
EM Software Task Software Package Version MOLECULAR REPLACEMENT CCP4 package
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE