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Crystal Structure of Mouse Cadherin-23 EC16-17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 0.1 M MMT pH 9.0
25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.861 α = 90 b = 90.861 β = 90 c = 170.68 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 PIXEL DECTRIS EIGER2 X 16M 2020-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 APS 24-ID-C
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 2.265 50 99 0.993 30.5 22.3 34006
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 2.265 2.31 89.5 0.777 3 12.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5WJM 2.265 48.267 33105 1654 97.242 0.211 0.2087 0.2109 0.2517 0.2527 60.786
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] -1.531 -1.531 3.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.614 r_dihedral_angle_4_deg 20.577 r_dihedral_angle_3_deg 14.16 r_dihedral_angle_1_deg 7.912 r_lrange_it 4.431 r_lrange_other 4.4 r_scangle_it 2.761 r_scangle_other 2.76 r_mcangle_it 2.209 r_mcangle_other 2.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.614 r_dihedral_angle_4_deg 20.577 r_dihedral_angle_3_deg 14.16 r_dihedral_angle_1_deg 7.912 r_lrange_it 4.431 r_lrange_other 4.4 r_scangle_it 2.761 r_scangle_other 2.76 r_mcangle_it 2.209 r_mcangle_other 2.208 r_scbond_it 1.73 r_scbond_other 1.729 r_angle_refined_deg 1.585 r_mcbond_it 1.456 r_mcbond_other 1.455 r_angle_other_deg 1.235 r_symmetry_xyhbond_nbd_refined 0.277 r_nbd_refined 0.198 r_nbd_other 0.188 r_symmetry_nbd_other 0.175 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.159 r_nbtor_refined 0.153 r_symmetry_xyhbond_nbd_other 0.092 r_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3270 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing