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Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M Sodium cacodylate pH 6.5,40% v/v MPD,5% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.276 α = 90 b = 50.613 β = 94.008 c = 88.263 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 EIGER X 16M 2022-12-16 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.63 50 93.6 0.074 0.091 0.052 0.997 10.956 2.8 54156
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 96.2 0.406 0.277 0.841 2.293 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.63 49.2 48084 2561 92.93 0.225 0.22276 0.22276 0.2303 0.27354 0.2805 23.224
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] -0.941 -0.434 -1.055 2.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.832 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_2_deg 11.068 r_dihedral_angle_1_deg 7.285 r_lrange_it 5.533 r_lrange_other 5.51 r_scangle_it 4.655 r_scangle_other 4.655 r_scbond_it 3.331 r_scbond_other 3.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.832 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_2_deg 11.068 r_dihedral_angle_1_deg 7.285 r_lrange_it 5.533 r_lrange_other 5.51 r_scangle_it 4.655 r_scangle_other 4.655 r_scbond_it 3.331 r_scbond_other 3.331 r_mcangle_it 3.226 r_mcangle_other 3.225 r_mcbond_it 2.545 r_mcbond_other 2.516 r_angle_refined_deg 1.703 r_angle_other_deg 0.579 r_symmetry_nbd_refined 0.267 r_nbd_other 0.245 r_nbd_refined 0.241 r_symmetry_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.159 r_metal_ion_refined 0.131 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3508 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing