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T1 domain of the renal potassium channel Kv1.3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QDW PDB ENTRY 1QDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 WE WANTED TO USE THE PROTEIN IN 150 MM POTASSIUM PHOSPHATE BUFFER PH 6.5 IN 5 MM NMR TUBES FOR CHARACTERIZATION USING NMR SPECTROSCOPY. DURING TESTING, WE OBSERVED THE FORMATION OF CRYSTALS IN THE NMR TUBES. AN INITIAL TEST OF THE CRYSTALS SHOWED AN EXCELLENT DIFFRACTION PATTERN, SO WE DECIDED TO CONTINUE WITH CRYSTALLIZATION OPTIMIZATION IN NMR TUBES, RESULTING IN VERY GOOD CRYSTALS
Crystal Properties Matthews coefficient Solvent content 2.2 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.74 α = 90 b = 59.74 β = 90 c = 62.33 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 MARRESEARCH DYNAMICALLY BENDABLE MIRROR 2005-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.2 45 99.2 0.05 17 3.7 33942
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 1.2 1.3 98.5 0.16 8.6 3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QDW 1.2 18.97 29377 1537 90.42 0.16499 0.16297 0.1658 0.20463 RANDOM 12.573
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] 0.22 0.22 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.199 r_dihedral_angle_4_deg 18.82 r_sphericity_free 13.454 r_dihedral_angle_3_deg 12.774 r_scangle_it 6.154 r_sphericity_bonded 5.726 r_dihedral_angle_1_deg 4.949 r_scbond_it 4.859 r_mcangle_it 3.632 r_mcbond_it 2.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.199 r_dihedral_angle_4_deg 18.82 r_sphericity_free 13.454 r_dihedral_angle_3_deg 12.774 r_scangle_it 6.154 r_sphericity_bonded 5.726 r_dihedral_angle_1_deg 4.949 r_scbond_it 4.859 r_mcangle_it 3.632 r_mcbond_it 2.873 r_rigid_bond_restr 2.566 r_angle_refined_deg 2.205 r_mcbond_other 1.281 r_angle_other_deg 1.18 r_symmetry_vdw_refined 0.366 r_symmetry_vdw_other 0.364 r_symmetry_hbond_refined 0.284 r_nbd_refined 0.252 r_nbd_other 0.22 r_nbtor_refined 0.199 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.155 r_nbtor_other 0.107 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 859 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing