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Crystal Structure of Mouse Cadherin-23 EC17-18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 277 0.1 M NaOAc pH 5.2
0.01 M MgCl2
25 % (v/v) MPD
25 mM 18-Crown-6
0.07 M CaCl2
Crystal Properties Matthews coefficient Solvent content 3.26 62.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.476 α = 90 b = 122.476 β = 90 c = 43.603 γ = 90
Symmetry Space Group P 43 21 2
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 0.97921 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 2.9 86.6 100 0.245 7.2 6 7803
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 2.9 2.95 99.5 0.833 1.72 4.6
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 (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 2wd0 2.9 86.6 7371 392 99.91 0.20326 0.19993 0.2055 0.26592 0.2678 RANDOM 27.858
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.585 r_dihedral_angle_3_deg 14.471 r_dihedral_angle_4_deg 13.836 r_dihedral_angle_1_deg 6.747 r_long_range_B_refined 4.873 r_long_range_B_other 4.872 r_scangle_other 3.075 r_mcangle_other 2.424 r_mcangle_it 2.418 r_scbond_it 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.585 r_dihedral_angle_3_deg 14.471 r_dihedral_angle_4_deg 13.836 r_dihedral_angle_1_deg 6.747 r_long_range_B_refined 4.873 r_long_range_B_other 4.872 r_scangle_other 3.075 r_mcangle_other 2.424 r_mcangle_it 2.418 r_scbond_it 1.76 r_scbond_other 1.759 r_angle_refined_deg 1.512 r_mcbond_it 1.398 r_mcbond_other 1.368 r_angle_other_deg 0.94 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1681 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing