☰ Navigation Tabs
Crystal Structure of Mouse Cadherin-23 EC9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TFL 5tfl,5i8d experimental model PDB 5I8D 5tfl,5i8d
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Magnesium Chloride
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.308 α = 90 b = 41.661 β = 114.196 c = 56.908 γ = 90
Symmetry Space Group P 1 21 1
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 2019-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 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 1.976 51.909 97 0.991 13.4 4.2 14817
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 2.03 0.907 4.8
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 5tfl,5i8d 1.976 51.909 14362 681 95.836 0.182 0.1802 0.1907 0.2241 0.2285 24.745
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] -1.676 -0.583 0.461 1.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.218 r_dihedral_angle_4_deg 17.085 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_1_deg 8.177 r_lrange_it 6.358 r_lrange_other 6.354 r_scangle_it 4.012 r_scangle_other 4.012 r_mcangle_it 3.721 r_mcangle_other 3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.218 r_dihedral_angle_4_deg 17.085 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_1_deg 8.177 r_lrange_it 6.358 r_lrange_other 6.354 r_scangle_it 4.012 r_scangle_other 4.012 r_mcangle_it 3.721 r_mcangle_other 3.72 r_scbond_other 2.543 r_scbond_it 2.54 r_mcbond_it 2.265 r_mcbond_other 2.256 r_angle_refined_deg 1.486 r_angle_other_deg 1.301 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.193 r_symmetry_nbd_other 0.181 r_metal_ion_refined 0.17 r_xyhbond_nbd_refined 0.161 r_nbtor_refined 0.15 r_nbd_other 0.133 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1617 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing