4BGC

T1 domain of the renal potassium channel Kv1.3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5WE 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 coefficientSolvent content
2.243.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.74α = 90
b = 59.74β = 90
c = 62.33γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHDYNAMICALLY BENDABLE MIRROR2005-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.24599.20.05173.733942
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.398.50.168.63

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QDW1.218.9729377153790.420.164990.162970.20463RANDOM12.573
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]
0.220.22-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.199
r_dihedral_angle_4_deg18.82
r_sphericity_free13.454
r_dihedral_angle_3_deg12.774
r_scangle_it6.154
r_sphericity_bonded5.726
r_dihedral_angle_1_deg4.949
r_scbond_it4.859
r_mcangle_it3.632
r_mcbond_it2.873
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.199
r_dihedral_angle_4_deg18.82
r_sphericity_free13.454
r_dihedral_angle_3_deg12.774
r_scangle_it6.154
r_sphericity_bonded5.726
r_dihedral_angle_1_deg4.949
r_scbond_it4.859
r_mcangle_it3.632
r_mcbond_it2.873
r_rigid_bond_restr2.566
r_angle_refined_deg2.205
r_mcbond_other1.281
r_angle_other_deg1.18
r_symmetry_vdw_refined0.366
r_symmetry_vdw_other0.364
r_symmetry_hbond_refined0.284
r_nbd_refined0.252
r_nbd_other0.22
r_nbtor_refined0.199
r_xyhbond_nbd_refined0.185
r_chiral_restr0.155
r_nbtor_other0.107
r_bond_refined_d0.028
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms859
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing