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Crystal structure of voltage-gated sodium channel NavAb V100C/Q150C disulfide crosslinked mutant in the activated state
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, HANGING DROP 4.8 277 1.8 M ammonium sulfate
0.1 M sodium citrate pH 4.8
Crystal Properties Matthews coefficient Solvent content 6.29 80.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.83 α = 90 b = 125.83 β = 90 c = 189.292 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 ADSC QUANTUM 315r 2016-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.89 50 97.9 0.125 0.13 0.035 1 22.06 12.9 16988 54.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 2.94 76.2 0.649 0.703 0.253 0.831 1.21 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3RVY 2.89 44.53 16065 923 97.64 0.2172 0.21421 0.2245 0.27317 0.2818 RANDOM 75.234
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] 3.42 3.42 -6.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.524 r_dihedral_angle_3_deg 20.986 r_dihedral_angle_4_deg 16.303 r_long_range_B_refined 14.135 r_long_range_B_other 14.135 r_scangle_other 11.54 r_mcangle_it 10.044 r_mcangle_other 10.04 r_scbond_it 7.256 r_scbond_other 7.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.524 r_dihedral_angle_3_deg 20.986 r_dihedral_angle_4_deg 16.303 r_long_range_B_refined 14.135 r_long_range_B_other 14.135 r_scangle_other 11.54 r_mcangle_it 10.044 r_mcangle_other 10.04 r_scbond_it 7.256 r_scbond_other 7.253 r_mcbond_it 6.743 r_mcbond_other 6.73 r_dihedral_angle_1_deg 6.401 r_angle_refined_deg 1.569 r_angle_other_deg 1.14 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1977 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 224
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building REFMAC refinement