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Crystal structure of voltage-gated sodium channel NavAb G94C/Q150C 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 5.6 277 1.8 M ammonium sulfate
0.1 M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 6.28 80.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.449 α = 90 b = 124.449 β = 90 c = 193.339 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 2018-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.000 ALS 8.2.2
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 2.75 50 94.8 0.117 0.12 0.026 1 27.75 19.6 19146 26.5
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 2.75 2.8 56.3 0.375 0.63 1 8.4
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 2.75 44.04 15906 851 83.24 0.21579 0.21321 0.2179 0.26543 0.2668 RANDOM 40.734
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] 0.1 0.1 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.14 r_dihedral_angle_3_deg 20.71 r_dihedral_angle_4_deg 20.125 r_long_range_B_refined 9.478 r_long_range_B_other 9.476 r_scangle_other 7.34 r_dihedral_angle_1_deg 6.884 r_mcangle_it 5.862 r_mcangle_other 5.86 r_scbond_it 4.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.14 r_dihedral_angle_3_deg 20.71 r_dihedral_angle_4_deg 20.125 r_long_range_B_refined 9.478 r_long_range_B_other 9.476 r_scangle_other 7.34 r_dihedral_angle_1_deg 6.884 r_mcangle_it 5.862 r_mcangle_other 5.86 r_scbond_it 4.597 r_scbond_other 4.596 r_mcbond_it 3.798 r_mcbond_other 3.788 r_angle_refined_deg 1.741 r_angle_other_deg 1.182 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 1817 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 342
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building REFMAC refinement