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Structure of the extracellular WNT-binding module in Drosophila Ror2/Nrk
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HKL 3HKL 1I71 experimental model PDB 1I71 3HKL 1I71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 294.15 3 mg/ml protein, 50 mM Bis-Tris propane (pH 5.0), 21% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.24 62.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.704 α = 90 b = 74.695 β = 106.31 c = 61.552 γ = 90
Symmetry Space Group C 1 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 2012-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9790 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.75 59.074 88.5 0.046 0.059 0.036 9.1 2.2 36932 36932
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 78 0.744 0.744 1.01 0.678 1 1.8
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 3HKL 1I71 1.75 42.5 1.34 36874 1802 87.79 0.1892 0.1873 0.1911 0.223 0.2263 41.7807
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 7.749 f_angle_d 1.202 f_chiral_restr 0.07 f_bond_d 0.013 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1833 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 46
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing