2NYJ

Crystal structure of the ankyrin repeat domain of TRPV1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52980.033MM PROTEIN, 5% PEG8000, 0.1M SODIUM CITRATE, 5MM ATP, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.7774.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.721α = 90
b = 124.721β = 90
c = 62.767γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-08-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418, 0.97907, 0.97922, 0.99298

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.23498.794121
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)
3.23.3199.90.0914.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT3.220845093598.90.240.2350.286RANDOM115.26
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]
2.421.212.42-3.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.984
r_dihedral_angle_4_deg22.189
r_dihedral_angle_3_deg20.854
r_dihedral_angle_1_deg5.698
r_angle_refined_deg1.237
r_scangle_it0.815
r_scbond_it0.479
r_mcangle_it0.403
r_nbtor_refined0.3
r_symmetry_hbond_refined0.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.984
r_dihedral_angle_4_deg22.189
r_dihedral_angle_3_deg20.854
r_dihedral_angle_1_deg5.698
r_angle_refined_deg1.237
r_scangle_it0.815
r_scbond_it0.479
r_mcangle_it0.403
r_nbtor_refined0.3
r_symmetry_hbond_refined0.279
r_nbd_refined0.231
r_mcbond_it0.217
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.166
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1893
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms31

Software

Software
Software NamePurpose
SOLVEphasing
REFMACrefinement