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Crystal Structure of Human Cadherin-23 EC6-8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 277 0.1 M MES pH 6.8, 1.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 4.12 70.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.407 α = 90 b = 93.407 β = 90 c = 122.386 γ = 120
Symmetry Space Group P 32 1 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 0.9792 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 2.92 80.89 99.9 0.079 17.08 4.2 13518
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 2.92 2.97 99.9 0.592 2 4.1
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 5TFL 2.92 80.89 12825 648 99.85 0.20006 0.19773 0.2008 0.24635 0.2491 RANDOM 88.416
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] 2.57 1.28 2.57 -8.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.891 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_4_deg 13.538 r_dihedral_angle_1_deg 6.102 r_long_range_B_refined 4.118 r_long_range_B_other 4.096 r_scangle_other 2.633 r_mcangle_it 2.576 r_mcangle_other 2.576 r_mcbond_it 1.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.891 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_4_deg 13.538 r_dihedral_angle_1_deg 6.102 r_long_range_B_refined 4.118 r_long_range_B_other 4.096 r_scangle_other 2.633 r_mcangle_it 2.576 r_mcangle_other 2.576 r_mcbond_it 1.542 r_mcbond_other 1.541 r_scbond_it 1.536 r_scbond_other 1.535 r_angle_refined_deg 1.428 r_angle_other_deg 0.895 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 2476 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing