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Structure of aquaporin-4 S180D mutant at 2.8 A resolution by electron crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6 293 10mM MES (pH 6.0), 75mM NaCl, 50mM MgCl2, 2mM DTT, 1% glycerol, MICRODIALYSIS, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69 α = 90 b = 69 β = 90 c = 160 γ = 90
Symmetry Space Group P 4 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 electron 4.2 CCD Tietz 2008-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ELECTRON MICROSCOPE OTHER 2.8
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.8 16.89 87 0.197 0.197 10057 8750
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 2.8 2.87 80.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2D57 2.8 10 9879 8089 481 81.88 0.234 0.234 0.23079 0.2448 0.28788 0.2994 RANDOM 52.335
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] -6.68 -6.68 13.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.615 r_dihedral_angle_3_deg 21.868 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_1_deg 6.297 r_sphericity_free 4.147 r_scangle_it 1.532 r_angle_refined_deg 1.524 r_mcangle_it 1.154 r_scbond_it 0.915 r_sphericity_bonded 0.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.615 r_dihedral_angle_3_deg 21.868 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_1_deg 6.297 r_sphericity_free 4.147 r_scangle_it 1.532 r_angle_refined_deg 1.524 r_mcangle_it 1.154 r_scbond_it 0.915 r_sphericity_bonded 0.777 r_rigid_bond_restr 0.731 r_mcbond_it 0.653 r_nbtor_refined 0.321 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.251 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1642 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement MRC data collection MRC data reduction MRC data scaling CNS phasing
Sample aquaporin-4 S180D mutant
Specimen Preparation Sample Aggregation State 2D ARRAY
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) Resolution Method Other Details Refinement Type Symmetry Type 2D CRYSTAL
Data Acquisition Detector Type GENERIC CCD Electron Dose (electrons/Å**2)
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL 3000SFF 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) 300 Imaging Details