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Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277 1.25 M Lithium Acetate,
0.1 M MES pH 7.2,
25% glycerol (cryo)
Crystal Properties Matthews coefficient Solvent content 6.96 82.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.994 α = 90 b = 164.657 β = 90 c = 183.634 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 PIXEL DECTRIS EIGER X 16M 2022-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 3.7 50 99.9 0.981 11.5 10.4 47174
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 3.7 3.76 99.6 0.56 1.96 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.716 49.563 47043 2329 98.678 0.189 0.1871 0.1915 0.2294 0.2294 124.855
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] 4.035 2.426 -6.461
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 40.939 r_lrange_other 40.939 r_scangle_it 36.624 r_scangle_other 36.622 r_mcangle_it 31.456 r_mcangle_other 31.454 r_scbond_it 27.759 r_scbond_other 27.757 r_dihedral_angle_2_deg 26.794 r_dihedral_angle_3_deg 23.336
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 40.939 r_lrange_other 40.939 r_scangle_it 36.624 r_scangle_other 36.622 r_mcangle_it 31.456 r_mcangle_other 31.454 r_scbond_it 27.759 r_scbond_other 27.757 r_dihedral_angle_2_deg 26.794 r_dihedral_angle_3_deg 23.336 r_mcbond_it 23.179 r_mcbond_other 23.166 r_dihedral_angle_6_deg 16.871 r_dihedral_angle_1_deg 7.428 r_angle_refined_deg 1.622 r_angle_other_deg 0.499 r_symmetry_nbd_refined 0.422 r_nbd_other 0.36 r_nbd_refined 0.275 r_metal_ion_refined 0.266 r_symmetry_nbd_other 0.238 r_nbtor_refined 0.198 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_other 0.081 r_chiral_restr 0.061 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10490 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing