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Crystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.1 M HEPES, pH 7.5, 0.1 M NaCl, 1.6 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.075 α = 90 b = 76.075 β = 90 c = 204.47 γ = 120
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 2013-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.4 47.37 99.5 0.046 0.026 0.999 14.5 4 25975
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 2.4 2.49 99.4 0.606 0.339 0.814 2.2 4.1 2724
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5BPB 2.4 65.88 24639 1322 99.43 0.2058 0.2037 0.2378 0.2429 0.2241 RANDOM 74.887
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] 0.66 0.33 0.66 -2.15
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.226 r_dihedral_angle_2_deg 36.074 r_dihedral_angle_3_deg 19.578 r_dihedral_angle_4_deg 15.154 r_dihedral_angle_1_deg 5.616 r_sphericity_bonded 4.654 r_mcangle_it 1.269 r_angle_refined_deg 1.075 r_mcbond_it 0.972 r_mcbond_other 0.971
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.226 r_dihedral_angle_2_deg 36.074 r_dihedral_angle_3_deg 19.578 r_dihedral_angle_4_deg 15.154 r_dihedral_angle_1_deg 5.616 r_sphericity_bonded 4.654 r_mcangle_it 1.269 r_angle_refined_deg 1.075 r_mcbond_it 0.972 r_mcbond_other 0.971 r_angle_other_deg 0.762 r_rigid_bond_restr 0.708 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3765 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction