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Crystal structure of voltage-gated sodium channel NavAb in high-pH condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 11% polyethylene glycol monomethyl ether 2000, 100 mM NaCl, 100 mM calcium nitrate, 100 mM Tris-HCl pH 8.4
Crystal Properties Matthews coefficient Solvent content 6.42 80.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.45 α = 90 b = 126.45 β = 90 c = 201.658 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 CCD RAYONIX MX225HE 2013-01-31 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) R Merge I (Observed) Rpim I (All) 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 31.47 87.68 0.248 0.087 14.02 9.1 20186 60.9798776849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 25.29 0.3136 1.074 9.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3RVY 2.8008556672 31.4605001582 1.33590617468 17985 921 87.778808141 0.231669922293 0.230018187795 0.2313 0.262134745718 0.2627 88.7405017713
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 24.1358211822 f_angle_d 1.32492732117 f_chiral_restr 0.0575773173154 f_bond_d 0.00960363017914 f_plane_restr 0.00660838643893
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1860 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 379
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing