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Structure of the extracellular WNT-binding module in Drl-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294.15 12 mg/ml protein, 100mM Tris (ph 8.5), 100 mM sodium acetate, 25% PEG 6000, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.978 α = 90 b = 91.583 β = 90 c = 76.362 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ Osmic mirrors 2012-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2 45.79 99.5 0.067 0.073 0.028 0.999 19.1 6.6 13786
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 2 2.05 94.2 0.898 1.048 0.524 0.597 3.6
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 THROUGHOUT 2YGN 2 29.97 1.33 13748 636 99.39 0.2315 0.2303 0.2289 0.2527 0.2505 46.0118
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 6.526 f_angle_d 0.625 f_chiral_restr 0.063 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1209 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing