☰ Navigation Tabs
Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 40% MPD, 0.2 M Lithium Chloride, 0.01 M Adenosine triphosphate disodium
Crystal Properties Matthews coefficient Solvent content 5.14 76.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.735 α = 90 b = 95.906 β = 90 c = 258.604 γ = 90
Symmetry Space Group P 2 2 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 PILATUS 6M-F 2018-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9790 APS 24-ID-C
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 2.99 50 99.9 0.208 9.31 10.2 48387
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 3 3.05 99.1 0.814 2.44 7.9
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 5T4M 2.99 47.95 45968 2321 98.32 0.17583 0.17397 0.1744 0.2138 0.2163 RANDOM 85.679
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] 16.44 -67.51 51.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.771 r_dihedral_angle_4_deg 18.121 r_dihedral_angle_3_deg 16.738 r_dihedral_angle_1_deg 8.154 r_long_range_B_refined 6.254 r_long_range_B_other 6.254 r_mcangle_it 4.215 r_mcangle_other 4.215 r_scangle_other 3.814 r_mcbond_it 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.771 r_dihedral_angle_4_deg 18.121 r_dihedral_angle_3_deg 16.738 r_dihedral_angle_1_deg 8.154 r_long_range_B_refined 6.254 r_long_range_B_other 6.254 r_mcangle_it 4.215 r_mcangle_other 4.215 r_scangle_other 3.814 r_mcbond_it 2.54 r_mcbond_other 2.54 r_scbond_it 2.288 r_scbond_other 2.288 r_angle_refined_deg 1.249 r_angle_other_deg 0.762 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 7966 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing