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Crystal Structure of the Voltage-Gated Sodium Channel NavMs in complex with 4-hydroxytamoxifen (2.4 Angstrom resolution)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1 M NaCl, 0.1 M CaCl2 dehydrate 0.1 M HEPES buffer, pH 6.5, 30 v/v polyethylene glycol (PEG) 400
Crystal Properties Matthews coefficient Solvent content 5.13 76.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.91 α = 90 b = 108.91 β = 90 c = 211.292 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 PIXEL DECTRIS PILATUS 6M 2019-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.9797 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 27.76 100 0.999 20.4 16.1 25305
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.976 3.8 15
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HVX 2.4 27.76 25285 1264 100 0.223 0.221 0.261 0.2435 RANDOM 89.57
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] -10.6278 -10.6278 21.2556
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.8 t_omega_torsion 2.56 t_angle_deg 0.98 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.8 t_omega_torsion 2.56 t_angle_deg 0.98 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2148 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 143
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing