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Crystal structure of voltage-gated sodium channel NavAb E32Q mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 10% polyethylene glycol monomethyl ether 2000, 100 mM NaCl, 100 mM calcium nitrate, 100 mM Tris-HCl, pH 8
Crystal Properties Matthews coefficient Solvent content 6.51 81.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.04 α = 90 b = 127.04 β = 90 c = 202.64 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 MX225-HS 2013-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.4 41.07 86.42 0.243 0.0689 0.998 14.86 13.9 11773 25.3055302345
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.521 1.924 0.543 0.845
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 5YUA 3.40003993335 41.0616138222 1.3777448541 10201 1020 86.5151386651 0.243872770287 0.240571490498 0.2428 0.272842668034 0.2763 61.1650526251
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 19.0231374819 f_angle_d 1.17123442856 f_chiral_restr 0.0650960318249 f_bond_d 0.0112629842162 f_plane_restr 0.00622383553357
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1865 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose phenix.refine refinement PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing