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Crystal Structure of Mouse Cadherin-23 EC13-15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K8R 5K8R,5WJ8 experimental model PDB 5WJ8 5K8R,5WJ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M HEPES pH7.5
0.2 M NaOAc
20% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.27 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.898 α = 90 b = 44.047 β = 94.586 c = 133.954 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.975 100 98 0.099 13.425 4.9 22984
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 1.975 2.01 97.4 0.209 9.44 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5K8R,5WJ8 1.975 44.548 22516 1104 97.637 0.177 0.175 0.1848 0.2212 0.2269 21.908
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] -0.423 -0.206 1.055 -0.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.056 r_dihedral_angle_4_deg 21.357 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 6.829 r_lrange_it 6.585 r_lrange_other 6.56 r_scangle_it 4.699 r_scangle_other 4.698 r_mcangle_it 3.157 r_mcangle_other 3.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.056 r_dihedral_angle_4_deg 21.357 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 6.829 r_lrange_it 6.585 r_lrange_other 6.56 r_scangle_it 4.699 r_scangle_other 4.698 r_mcangle_it 3.157 r_mcangle_other 3.156 r_scbond_it 2.972 r_scbond_other 2.971 r_mcbond_it 2.075 r_mcbond_other 2.075 r_angle_refined_deg 1.664 r_angle_other_deg 1.421 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.205 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.16 r_nbd_other 0.159 r_metal_ion_refined 0.09 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2304 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing