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Crystal Structure of Human Protocadherin-24 EC1-2 Form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.2 MM NaI
20% PEG3350
CDHR5 EC1-2
Crystal Properties Matthews coefficient Solvent content 2.71 54.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.899 α = 90 b = 86.641 β = 103.458 c = 104.892 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 2020-12-01 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) 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 3.175 50 96.3 0.987 5.6 3.5 18809
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 3.175 3.23 89.1 0.277 2.63 2.5
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 5CZR 3.175 49.147 18083 862 95.219 0.217 0.2135 0.2163 0.2896 0.2885 41.168
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] -0.375 -1.706 0.913 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.531 r_dihedral_angle_3_deg 19.808 r_lrange_it 15.899 r_lrange_other 15.899 r_dihedral_angle_4_deg 15.786 r_scangle_it 11.386 r_scangle_other 11.385 r_mcangle_it 8.466 r_mcangle_other 8.465 r_scbond_it 7.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.531 r_dihedral_angle_3_deg 19.808 r_lrange_it 15.899 r_lrange_other 15.899 r_dihedral_angle_4_deg 15.786 r_scangle_it 11.386 r_scangle_other 11.385 r_mcangle_it 8.466 r_mcangle_other 8.465 r_scbond_it 7.766 r_scbond_other 7.766 r_dihedral_angle_1_deg 7.231 r_mcbond_it 5.469 r_mcbond_other 5.467 r_angle_refined_deg 2.02 r_angle_other_deg 1.489 r_nbd_other 0.323 r_metal_ion_refined 0.313 r_symmetry_nbd_refined 0.297 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_refined 0.244 r_symmetry_nbd_other 0.226 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.137 r_symmetry_nbtor_other 0.108 r_chiral_restr 0.073 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6500 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing