☰ Navigation Tabs
A Rare Lysozyme Crystal Form Solved Using High-Redundancy 3D Electron Diffraction Data from Micron-Sized Needle Shaped Crystals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.72 α = 90 b = 103.88 β = 90 c = 31.65 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 97
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 28.68 79.7 42.4 9516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 64.3 25.9
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) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 1AKI 2.2 28.673 1.35 9516 476 79.73 0.2382 0.2365 0.2641 0.27 0.3033 Random 34.77
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 18.762 f_angle_d 0.55 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.002
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing
Sample 3D crystals of Lysozyme C from Gallus gallus
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) 2.2 Resolution Method OTHER Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 67.72 Length b 103.88 Length c 103.88 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 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 REFINEMENT PHENIX 1.11.1 MODEL REFINEMENT Coot 0.8.8 MOLECULAR REPLACEMENT PHASER 2.7.16 CRYSTALLOGRAPHY MERGING XSCALE Nov 1, 2016
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE