3OTF

Structural basis for the cAMP-dependent gating in human HCN4 channel


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q43PDB ENTRY 1Q43

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529812% ethanol, sodium citrate, 200 mM Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.3848.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.264α = 90
b = 69.264β = 90
c = 191.616γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.97923NSLSX4C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.450940.0530.0539567
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4495.90.2775.28.4

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 1Q432.450854943393.860.238570.236740.27464RANDOM79.065
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]
-0.5-0.50.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.351
r_dihedral_angle_4_deg25.44
r_dihedral_angle_3_deg18.068
r_dihedral_angle_1_deg4.843
r_angle_refined_deg1.082
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other
r_nbd_refined
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.351
r_dihedral_angle_4_deg25.44
r_dihedral_angle_3_deg18.068
r_dihedral_angle_1_deg4.843
r_angle_refined_deg1.082
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1561
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling