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Crystal structure of the first WW domain of human YAP2 isoform
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 293 1.5 M ammonium sulphate, 0.1 M sodium acetate, 100 mM proline, 5 mM NDSB-201 and 5mM MBCD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.77 30.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.673 α = 90 b = 43.101 β = 90 c = 21.302 γ = 90
Symmetry Space Group P 21 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 SI(111) CHANNEL-CUT CRYSTAL MONOCHROMATOR AND A PAIR OF KB MIRRORS 2013-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.6 42.67 99.2 0.104 0.104 12 6.9 5514 12.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 96.9 0.582 3.2 6.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2HO2 1.6 21.551 0.47 10001 9891 452 98.83 0.1785 0.1776 0.1804 0.1942 0.1918 16.7
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 14.606 f_angle_d 1.356 f_chiral_restr 0.056 f_bond_d 0.011 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 378 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 5
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction autoPROC data scaling