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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 5 277 0.33mM protein, 9% PEG8000, 0.1M sodium citrate, pH 5.0, 5-7% xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.514 α = 90 b = 95.862 β = 90 c = 164.504 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 CCD ADSC QUANTUM 4 2004-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM 0.97922 APS 8-BM
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.1 48 99.7 0.14 0.1 17.4 6.7 11981 11944 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.1 3.21 100 0.493 0.447 5.3 7.1
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 3.1 20 11944 10738 1170 99.89 0.307 0.21499 0.20979 0.2353 0.26184 0.2677 RANDOM 40.874
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] 2.57 -1.1 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.493 r_dihedral_angle_3_deg 16.859 r_dihedral_angle_4_deg 15.056 r_dihedral_angle_1_deg 4.757 r_angle_refined_deg 0.961 r_scangle_it 0.646 r_scbond_it 0.371 r_mcangle_it 0.323 r_nbtor_refined 0.293 r_symmetry_hbond_refined 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.493 r_dihedral_angle_3_deg 16.859 r_dihedral_angle_4_deg 15.056 r_dihedral_angle_1_deg 4.757 r_angle_refined_deg 0.961 r_scangle_it 0.646 r_scbond_it 0.371 r_mcangle_it 0.323 r_nbtor_refined 0.293 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.191 r_mcbond_it 0.174 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 3896 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing