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Crystal Structure of Human Mucin-like Protocadherin EC1-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.4 277 0.1M Sodium Acetate pH 4.4, 0.7M Calcium Chloride
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.427 α = 90 b = 78.379 β = 90 c = 121.39 γ = 90
Symmetry Space Group I 2 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 EIGER X 16M 2019-03-03 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) 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 1.9 50 99.7 0.074 46.14 24.1 19398
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 1.9 1.93 99.7 0.263 14.5 21.8
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 (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 5UZ8 1.9 46.61 18379 948 99.49 0.19887 0.197 0.203 0.23414 0.2414 RANDOM 28.323
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] -1.45 4.14 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.793 r_dihedral_angle_4_deg 22.28 r_dihedral_angle_3_deg 12.608 r_dihedral_angle_1_deg 6.357 r_long_range_B_refined 4.757 r_long_range_B_other 4.716 r_scangle_other 3.241 r_mcangle_it 2.522 r_mcangle_other 2.522 r_scbond_it 2.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.793 r_dihedral_angle_4_deg 22.28 r_dihedral_angle_3_deg 12.608 r_dihedral_angle_1_deg 6.357 r_long_range_B_refined 4.757 r_long_range_B_other 4.716 r_scangle_other 3.241 r_mcangle_it 2.522 r_mcangle_other 2.522 r_scbond_it 2.003 r_scbond_other 2.002 r_mcbond_it 1.551 r_mcbond_other 1.543 r_angle_refined_deg 1.531 r_angle_other_deg 1.253 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 1616 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing