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MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KTZ PDB entry 1KTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.5 ul 20 mg/mL protein + 0.25 ul mother liquor + 0.2 ul seed stock in 100 mM HEPES/NaOH pH 7.5, 45% MPD
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.53 α = 90 b = 71.33 β = 90 c = 79.508 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 293 CMOS TVIPS TEMCAM-F416 2016-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ELECTRON MICROSCOPE OTHER 0.0250793397
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.9 26.64 71.9 0.293 0.293 0.951 3.3 3.8 3884 64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.07 71.3 2.024 0.255 0.8 3.9
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-Free (Depositor) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 1KTZ 2.9 26.64 3848 290 68.82 0.2948 0.2919 0.328
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 19.181 f_angle_d 1.573 f_chiral_restr 0.067 f_bond_d 0.012 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1327 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing
Sample Complex between monomeric TGF-b and its receptor, TbRII
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) 2.9 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 41.5298 Length b 71.3297 Length c 71.3297 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TVIPS TEMCAM-F416 (4k x 4k) Electron Dose (electrons/Å**2) 0.004
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI F20 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 IMAGE ACQUISITION EM-Menu 4.0.9.75 DIFFRACTION INDEXING iMosflm/MOSFLM 7.2.1 MODEL FITTING Phaser 2.6.0 OTHER MOLREP 11.4.05 MODEL REFINEMENT PHENIX 1.10 MOLECULAR REPLACEMENT Phaser 2.6.0 SYMMETRY DETERMINATION POINTLESS 1.10.26 CRYSTALLOGRAPHY MERGING AIMLESS 0.5.27
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE