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Crystal Structure of the N-terminal PAS domain from the hERG3 Potassium Channel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 hERG3 PAS domain (15 mg/ml, in 50 mM NaCl, 1 mM TCEP in a 1:1 ratio with reservoir solution (0.1 M NaCl, 0.1 M HEPES pH=7.5, 1.6 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 1.75 29.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.784 α = 90 b = 32.784 β = 90 c = 200.681 γ = 90
Symmetry Space Group P 43 21 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 PILATUS3 6M 2017-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
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 1.39 66.9 100 0.061 13.9 11.9656537283 23496
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 1.39 1.43 0.766
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4HQA 1.39 50.221 22170 1208 99.983 0.187 0.1843 0.1743 0.2352 0.2353 32.173
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] -1.748 -1.748 3.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.003 r_dihedral_angle_4_deg 27.681 r_dihedral_angle_3_deg 18.961 r_rigid_bond_restr 18.195 r_scangle_it 9.461 r_scangle_other 9.454 r_lrange_it 9.05 r_lrange_other 9 r_scbond_it 7.991 r_scbond_other 7.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.003 r_dihedral_angle_4_deg 27.681 r_dihedral_angle_3_deg 18.961 r_rigid_bond_restr 18.195 r_scangle_it 9.461 r_scangle_other 9.454 r_lrange_it 9.05 r_lrange_other 9 r_scbond_it 7.991 r_scbond_other 7.985 r_dihedral_angle_1_deg 7.135 r_mcangle_it 5.435 r_mcangle_other 5.432 r_mcbond_it 4.598 r_mcbond_other 4.569 r_angle_refined_deg 2.234 r_angle_other_deg 1.646 r_symmetry_nbd_refined 0.665 r_nbd_other 0.618 r_symmetry_xyhbond_nbd_refined 0.301 r_symmetry_nbd_other 0.257 r_nbd_refined 0.236 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.124 r_symmetry_nbtor_other 0.093 r_bond_refined_d 0.02 r_gen_planes_refined 0.016 r_bond_other_d 0.01 r_gen_planes_other 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 937 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing