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Crystal structure of voltage-gated sodium channel NavAb N49K mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 7%-9% PEG 6000, 100mM sodium chloride, 100mM magnesium nitrate, 100mM cadmium nitrate, 10mM copper chloride, 100mM Tris-HCl, pH 8.4
Crystal Properties Matthews coefficient Solvent content 7.9 84.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128 α = 90 b = 128 β = 90 c = 203.18 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2024-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
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 3.8 45.25 99.64 0.04986 0.997 16.93 31 8644 120.42
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) 1 3.8 3.9 0.9918 0.884
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.8 45.25 1.38 8629 433 99.64 0.2988 0.2981 0.2995 0.3148 0.3212 156.32
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 15.8551 f_angle_d 1.5304 f_chiral_restr 0.0757 f_bond_d 0.0121 f_plane_restr 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1778 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 434
Software Software Software Name Purpose PHENIX refinement XDS data reduction DIALS data scaling PHENIX phasing