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Crystal structure of the NavAb voltage-gated sodium channel (wild-type, 3.2 A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RVY pdb entry 3RVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.75 298 CHAPSO:DMPC BICELLES, 2 M AMMONIUM SULPHATE, 0.1 M NA-CITRATE, 28% GLUCOSE, NICOTINIC ACID, pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 5.65 78.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.856 α = 90 b = 125.856 β = 90 c = 192.641 γ = 90
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 315 2011-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9792 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.21 50 96.44 0.086 3 44951 44951 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 99.4 0.676 1.05 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 3RVY 3.21 50 44951 44951 2397 96.44 0.30861 0.30861 0.3079 0.3137 0.32168 0.3218 RANDOM 102.725
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] 53.81 53.81 -107.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.968 r_dihedral_angle_3_deg 18.899 r_dihedral_angle_4_deg 16.323 r_dihedral_angle_1_deg 5.699 r_angle_refined_deg 1.382 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7138 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 77
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building REFMAC refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing