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Crystal structure of human delta protocadherin 17 EC1-EC4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296 13%(w/v) PEG 4000
0.3M NaCl
0.1M MES pH 6.5
30% PEG 400 (v/v) added as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 3.09 60.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 214.55 α = 90 b = 105.838 β = 101.038 c = 101.403 γ = 90
Symmetry Space Group C 1 2 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 2016-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 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 3.7 40 96.7 0.211 0.248 0.128 1 5.4 3.5 22957 92.4422118318
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.7 4 92.1 0.735 0.866 0.451 0.71 1.6 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 6VFQ 3.71 19.94 1.34 22795 1133 96.33 0.2552 0.2528 0.2568 0.3002 0.2983 Random selection 128.02
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.0009098716 f_angle_d 0.821108236417 f_chiral_restr 0.0520180182726 f_bond_d 0.00791959686657 f_plane_restr 0.00479918764635
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12825 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 499
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing