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Structure of lens aquaporin-0 array in sphingomyelin/cholesterol bilayer (1SM:2Chol)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B6O
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.5 α = 90 b = 65.5 β = 90 c = 200 γ = 90
Symmetry Space Group P 4 2 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) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 2.35 2.5 1.33 17031 1704 90.19 0.2642 0.2617 0.2823 0.2866 0.3053 Random selection 51.15
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 15.071 f_angle_d 0.8381 f_chiral_restr 0.0374 f_bond_d 0.0053 f_plane_restr 0.0046
Software Software Software Name Purpose phenix.refine refinement PHENIX refinement PHASER phasing IPLT data reduction
Sample Lens aquaporin-0 in sphingomyelin/cholesterol bilayer
Specimen Preparation Sample Aggregation State 2D ARRAY Embedding Material Trehalose Embedding Details Aquaporin-0 2D crystals were prepared on molybdenum grids using the carbon sandwich method and a trehalose concentration ranging from 3% to 5% (w/v).
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 2.35 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 2D CRYSTAL Space Group Name P 4 2 2 Length a 65.5 Length b 65.5 Angle Gamma 90 Space Group Name P 4 2 2 Length a 65.5 Length b 65.5 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (2B6O) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN ULTRASCAN 4000 (4k x 4k) Electron Dose (electrons/Å**2) 10
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI POLARA 300 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model OTHER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details The diffraction patterns were recorded without setting defocus.
EM Software Task Software Package Version IMAGE ACQUISITION DigitalMicrograph 2 MOLECULAR REPLACEMENT CCP4 package 6.0 CRYSTALLOGRAPHY MERGING IPET 0.9.8 RECONSTRUCTION IPET 0.9.8 MODEL REFINEMENT CNS 1.3 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE