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Crystal structure of human protocadherin 19 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 7%(w/v) PEG 4000
0.2M NaCl
0.05M MES pH6.5
15% (v/v) 2R,3R-butanediol added as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 3.81 67.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.971 α = 90 b = 108.971 β = 90 c = 309.663 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M-F 2016-06-29 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 3.5 40 99.9 0.14 0.15 0.047 1 9.4 9.8 27770 138.742878931
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 3.5 3.71 99.9 2.5 2.6 0.814 0.72 1.1 10.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6VFQ 3.5 19.99 1.34 27515 1377 99.8 0.2661 0.2648 0.2716 0.2915 0.3084 193.423073948
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 10.109319698 f_angle_d 0.790529019265 f_chiral_restr 0.0537826150494 f_bond_d 0.00935663952743 f_plane_restr 0.00488673203645
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9737 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 176
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing