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Crystal Structure of Human Cadherin-23 EC13-14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.1 M NaOAc pH 4.5
0.2 M CaCl2
30 (v/v) isopropanol
20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.48 64.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.712 α = 90 b = 74.712 β = 90 c = 213.507 γ = 120
Symmetry Space Group P 62 2 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 2017-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 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 1.86 71.17 94.4 0.076 26.8 10.2 30738
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 1.86 1.89 83.3 0.538 2 7.1
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 5VH2 1.86 71.17 27574 1422 94.56 0.21843 0.2169 0.2227 0.24828 0.2545 RANDOM 45.936
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] 1.66 0.83 1.66 -5.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_dihedral_angle_4_deg 16.959 r_dihedral_angle_3_deg 11.421 r_long_range_B_refined 6.008 r_dihedral_angle_1_deg 5.935 r_long_range_B_other 5.887 r_scangle_other 1.609 r_angle_refined_deg 1.5 r_mcangle_it 1.454 r_mcangle_other 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_dihedral_angle_4_deg 16.959 r_dihedral_angle_3_deg 11.421 r_long_range_B_refined 6.008 r_dihedral_angle_1_deg 5.935 r_long_range_B_other 5.887 r_scangle_other 1.609 r_angle_refined_deg 1.5 r_mcangle_it 1.454 r_mcangle_other 1.453 r_angle_other_deg 0.982 r_scbond_it 0.95 r_scbond_other 0.947 r_mcbond_it 0.868 r_mcbond_other 0.868 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 1610 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing