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Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 3.5 M Ammonium chloride
0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.6 73.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.446 α = 90 b = 168.834 β = 90 c = 125.276 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 CCD ADSC QUANTUM 315 2016-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97920 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 2.588 50 99.9 0.091 18.1 6.1 39416
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 2.588 2.63 99.5 1.022 1.75 5.8
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 2WHV 2.588 48.529 39346 1913 99.643 0.206 0.204 0.2067 0.2461 0.2464 58.957
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] -4.191 0.706 3.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.797 r_dihedral_angle_4_deg 19.426 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_1_deg 7.968 r_lrange_it 5.489 r_lrange_other 5.489 r_scangle_it 3.205 r_scangle_other 3.204 r_mcangle_it 2.705 r_mcangle_other 2.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.797 r_dihedral_angle_4_deg 19.426 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_1_deg 7.968 r_lrange_it 5.489 r_lrange_other 5.489 r_scangle_it 3.205 r_scangle_other 3.204 r_mcangle_it 2.705 r_mcangle_other 2.704 r_scbond_it 1.962 r_scbond_other 1.962 r_mcbond_it 1.698 r_mcbond_other 1.698 r_angle_refined_deg 1.554 r_angle_other_deg 1.222 r_nbd_other 0.233 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.18 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.153 r_metal_ion_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4776 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing