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Crystal Structure of Mouse Cadherin-23 EC25-26
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VT8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 0.1 M HEPES ph 7.8
0.35 M CaCl2
28 % PEG 400
Crystal Properties Matthews coefficient Solvent content 3.35 63.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.237 α = 90 b = 88.488 β = 90 c = 206.783 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2020-11-01 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) CC (Half) 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 2.248 45.055 98.7 0.968 11.08 9.1 35493
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.248 2.3 84.4 0.894 4.7 7.3
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 5VT8 2.248 45.055 34971 1730 98.602 0.2 0.1976 0.2019 0.2533 0.254 37.253
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] 0.953 0.199 -1.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.46 r_dihedral_angle_4_deg 18.819 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_1_deg 8.179 r_lrange_it 7.379 r_lrange_other 7.353 r_scangle_it 5.851 r_scangle_other 5.851 r_mcangle_other 4.5 r_mcangle_it 4.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.46 r_dihedral_angle_4_deg 18.819 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_1_deg 8.179 r_lrange_it 7.379 r_lrange_other 7.353 r_scangle_it 5.851 r_scangle_other 5.851 r_mcangle_other 4.5 r_mcangle_it 4.499 r_scbond_it 3.908 r_scbond_other 3.902 r_mcbond_it 3.178 r_mcbond_other 3.177 r_angle_refined_deg 1.593 r_angle_other_deg 1.262 r_symmetry_nbd_refined 0.311 r_nbd_refined 0.245 r_metal_ion_refined 0.204 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.161 r_symmetry_metal_ion_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3717 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing