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Crystal structure of human protocadherin 1 EC1-EC4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DZQ 5DZQ, 4ZPL experimental model PDB 4ZPL 5DZQ, 4ZPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 296 8.5% (w/v) PEG 4000, 20% (v/v) glycerol, 0.1M tris-bicine buffer pH8.5, 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine
Crystal Properties Matthews coefficient Solvent content 4.99 75.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.595 α = 90 b = 148.595 β = 90 c = 149.846 γ = 120
Symmetry Space Group P 61 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 PILATUS 6M-F 2016-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 3.2 40 100 0.12 0.12 0.028 1 15.9 18.3 16684 115.50962728
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 3.2 3.42 100 1.685 1.73 0.394 0.81 2.1 19.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5DZQ, 4ZPL 3.2 19.87 1.34 16561 827 99.96 0.224 0.2218 0.2336 0.264 0.2673 144.64
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 10.3221368712 f_angle_d 0.541085929824 f_chiral_restr 0.0449182984195 f_bond_d 0.00842605308763 f_plane_restr 0.00343972033694
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3365 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing