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Crystal structure of the Protocadherin GammaB4 extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V5X 5V5X, 5T9T experimental model PDB 5T9T 5V5X, 5T9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 295 10% (w/v) PEG8000, 20% ethylene glycol, 10% Morpheus Amino Acids (Molecular Dimensions), and 0.1 M Morpheus Buffer System 2 (Hepes/MOPS buffer; Molecular Dimensions) pH 7.5
Crystal Properties Matthews coefficient Solvent content 5.55 77.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.73 α = 90 b = 87.58 β = 109.94 c = 149.33 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 PILATUS 6M-F 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97919 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 4.5 40 93.4 0.113 0.138 0.078 0.995 5.2 2.8 8694 66.09
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 4.5 5.05 0.173 0.211 0.119 0.973 5.7 3
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 5V5X, 5T9T 4.52 38.29 1.35 8683 448 93.4 0.2336 0.2312 0.2385 0.2767 0.2824 138.7
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 11.5773 f_angle_d 0.5654 f_chiral_restr 0.0417 f_plane_restr 0.0038 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9489 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 253
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing