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Crystal structure of Frizzled 7 CRD in complex with F7.B Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 10 293 0.1 M CAPS, pH 10.5,
20% (w/v) PEG 3350,
0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.544 α = 90 b = 103.446 β = 90 c = 144.207 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX-300 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 38.551 99.9 0.124 0.049 0.998 12.6 7.3 37237
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 1.12 0.438 0.701
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 5bpq 2.1 38.551 1.33 37227 1862 99.95 0.1943 0.1919 0.1937 0.2417 0.2394
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 17.412 f_angle_d 0.94 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4201 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement XPREP data reduction XDS data scaling PHENIX phasing