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Crystal structure of NavAb L101S as a basis for the human Nav1.7 Inherited Erythromelalgia F216S mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MWA 6MWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 277 1.7-1.8 M Ammonium Sulfate
0.1 M Sodium Citrate pH 4.8
Crystal Properties Matthews coefficient Solvent content 6.26 80.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.06 α = 90 b = 125.06 β = 90 c = 190.743 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 2021-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
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 2.85 50 99.7 0.153 0.059 0.994 13.5 7.5 17973 75.31
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 2.85 2.9 96.9 1.344 0.674 0.548 4.3
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 6MWA 2.85 41.99 1.36 17968 860 99.6 0.2238 0.2223 0.2222 0.2535 0.2501 86.32
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 12.7455 f_angle_d 1.0357 f_chiral_restr 0.0588 f_bond_d 0.0087 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1969 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 219
Software Software Software Name Purpose BOS data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building PHENIX refinement