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Human protocadherin 10 ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VFV 6VFV, 6VFQ experimental model PDB 6VFQ 6VFV, 6VFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 296 0.22M CaCl2, 0.1M Na Acetate pH 5.0 with 30% (v/v) glycerol as cryoprotectant and glutaraldehyde (0.5% v/v) added to the reservoir after crystal formation to aid crystal stability by cross-linking
Crystal Properties Matthews coefficient Solvent content 6.72 81.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.087 α = 90 b = 84.087 β = 90 c = 543.917 γ = 90
Symmetry Space Group P 41 21 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 2016-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 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 3.298 40 99.7 0.139 0.145 0.04 1 10.7 12.9 19779 62.4073673952
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 3.298 3.48 99.5 2.475 2.57 0.687 0.95 1.6 13.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6VFV, 6VFQ 3.298 20 1.34 19771 1001 64.28 0.2297 0.22687 0.2843 0.2683 random 108.52
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 12.5803044139 f_angle_d 0.67350529932 f_chiral_restr 0.0454112738884 f_bond_d 0.0104931771821 f_plane_restr 0.00328642215886
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5012 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 128
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing