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Crystal structure of a voltage-gated K+ channel pore domain in a closed state in lipid membranes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EFF PDB ENTRY 3EFF, 2ATK , 2A79 AND 1ORQ experimental model PDB 2ATK PDB ENTRY 3EFF, 2ATK , 2A79 AND 1ORQ experimental model PDB 2A79 PDB ENTRY 3EFF, 2ATK , 2A79 AND 1ORQ experimental model PDB 1ORQ PDB ENTRY 3EFF, 2ATK , 2A79 AND 1ORQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.25 293 25% (v/v) PEG-MME-550, 0.35 M sodium nitrate, 50 mM ADA, 50 mM sodium malonate pH 7.0, Lipidic Cubic Phase (LCP), temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.1 α = 90 b = 80.67 β = 90 c = 55.522 γ = 90
Symmetry Space Group P 21 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 CCD MARMOSAIC 300 mm CCD 2011-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 3.35 32.6 95.2 0.116 15.8 5.8 3736 101.9
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 3.35 3.47 86 0.66 1.1 4.8
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 PDB ENTRY 3EFF, 2ATK , 2A79 AND 1ORQ 3.35 32.6 3736 534 95.5 0.318 0.314 0.3329 0.341 0.3527 RANDOM 192.51
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] 9.2681 36.1359 -45.404
RMS Deviations Key Refinement Restraint Deviation t_angle_deg 0.94 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_omega_torsion
RMS Deviations Key Refinement Restraint Deviation t_angle_deg 0.94 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_omega_torsion t_other_torsion t_improper_torsion 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 1303 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling