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Crystal Structure of Mouse Cadherin-23 EC8-9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TFL 5tfl,5tfk experimental model PDB 5TFK 5tfl,5tfk
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M NaCl
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.827 α = 90 b = 56.194 β = 90 c = 93.853 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2018-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.966 48.213 98.9 0.966 7.75 8.8 4947
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.97 3.02 95.3 0.809 1.77 4.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5tfl,5tfk 2.966 48.213 4864 253 98.761 0.218 0.2139 0.2992 0.3022 52.1
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] -3.865 6.044 -2.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.953 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_4_deg 12.254 r_dihedral_angle_1_deg 5.942 r_lrange_it 4.858 r_lrange_other 4.856 r_mcangle_other 2.945 r_mcangle_it 2.944 r_scangle_it 2.271 r_scangle_other 2.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.953 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_4_deg 12.254 r_dihedral_angle_1_deg 5.942 r_lrange_it 4.858 r_lrange_other 4.856 r_mcangle_other 2.945 r_mcangle_it 2.944 r_scangle_it 2.271 r_scangle_other 2.271 r_mcbond_it 1.66 r_mcbond_other 1.643 r_angle_refined_deg 1.442 r_scbond_it 1.276 r_scbond_other 1.275 r_angle_other_deg 1.07 r_nbd_refined 0.198 r_symmetry_nbd_other 0.141 r_nbd_other 0.141 r_nbtor_refined 0.136 r_xyhbond_nbd_refined 0.132 r_metal_ion_refined 0.125 r_symmetry_nbd_refined 0.101 r_symmetry_nbtor_other 0.063 r_chiral_restr 0.042 r_symmetry_xyhbond_nbd_refined 0.02 r_bond_refined_d 0.011 r_bond_other_d 0.004 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1614 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing