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MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 295 0.1 M Bis-Tris Propane, 1.1 M LiSO4
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.614 α = 90 b = 122.552 β = 96.55 c = 78.704 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 electron M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ELECTRON MICROSCOPE 0.0251
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 3 27.5 79.8 0.255 0.9 3 5.7 10480 55.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.2 78.7 1.324 0.35 0.7 5.7 1006
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-Free (Depositor) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT THROUGHOUT 5i4t 3 19.863 1.34 10477 1049 78.6 0.2576 0.2536 0.2916 46.1189
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 11.344 f_angle_d 0.561 f_chiral_restr 0.034 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3805 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction
Sample CTD-SP1 fragment of HIV-1 Gag
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument FEI VITROBOT MARK IV 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 70.61 Length b 122.55 Length c 122.55 Angle Alpha 96.55 Angle Beta 90 Angle Gamma 96.55
Map-Model Fitting and Refinement Id 1 (5I4T) Refinement Space RECIPROCAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 41.1 Fitting Procedure Details
Data Acquisition Detector Type TVIPS TEMCAM-F416 (4k x 4k) Electron Dose (electrons/Å**2) 0.05
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 MOLECULAR REPLACEMENT PHENIX dev-2747 CRYSTALLOGRAPHY MERGING AIMLESS MODEL REFINEMENT PHENIX dev-2747
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE