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Crystal structure of the ankyrin repeat domain of TRPV2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ETA PDB ENTRY 2ETA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 0.17mM protein, 1.2M lithium acetate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.954 α = 90 b = 57.476 β = 90 c = 139.433 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.6 35 99.7 0.057 11.2 4.38 44382 44271 1 1
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) 1.6 1.66 78.1 0.443 2.5 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2ETA 1.65 20 42272 35381 3930 97.07 0.215 0.18912 0.18547 0.197 0.22194 0.23 RANDOM 22.053
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] -1.57 1.74 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.42 r_dihedral_angle_3_deg 12.726 r_dihedral_angle_4_deg 12.637 r_dihedral_angle_1_deg 5.464 r_scangle_it 3.669 r_scbond_it 2.425 r_angle_refined_deg 1.424 r_mcangle_it 1.347 r_mcbond_it 0.865 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.42 r_dihedral_angle_3_deg 12.726 r_dihedral_angle_4_deg 12.637 r_dihedral_angle_1_deg 5.464 r_scangle_it 3.669 r_scbond_it 2.425 r_angle_refined_deg 1.424 r_mcangle_it 1.347 r_mcbond_it 0.865 r_nbtor_refined 0.298 r_symmetry_hbond_refined 0.263 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 1951 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOLREP phasing