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Crystal Structure of Mouse Cadherin-23 EC7+8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I8D Cadherin-23 (5I8D)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.7 277 0.1 M Sodium Acetate pH 4.7, 1.9 M Sodium Chloride, 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 5.24 76.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.809 α = 90 b = 185.809 β = 90 c = 185.809 γ = 90
Symmetry Space Group P 41 3 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 PIXEL DECTRIS PILATUS 6M-F 2015-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97921 APS 24-ID-C
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 3.56 131.39 100 0.363 20 35.5 13716 87.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.56 3.61 100 1.587 0.748 2.5 23.7
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 Cadherin-23 (5I8D) 3.56 131.39 12849 666 98.9 0.19385 0.19238 0.1942 0.22143 0.2224 RANDOM 90.48
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 41.9 r_dihedral_angle_3_deg 18.853 r_dihedral_angle_4_deg 14.703 r_dihedral_angle_1_deg 10.022 r_long_range_B_refined 7.005 r_long_range_B_other 7.004 r_scangle_other 4.904 r_mcangle_it 4.479 r_mcangle_other 4.478 r_scbond_it 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.9 r_dihedral_angle_3_deg 18.853 r_dihedral_angle_4_deg 14.703 r_dihedral_angle_1_deg 10.022 r_long_range_B_refined 7.005 r_long_range_B_other 7.004 r_scangle_other 4.904 r_mcangle_it 4.479 r_mcangle_other 4.478 r_scbond_it 2.97 r_scbond_other 2.969 r_mcbond_it 2.739 r_mcbond_other 2.73 r_angle_refined_deg 1.365 r_angle_other_deg 0.784 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 3084 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing