☰ Navigation Tabs
Crystal structure of human Frizzled 4 Cysteine-Rich Domain (CRD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 1.8 M ammonium sulfate, 0.1 M tri-Na citrate pH 5.6 and 0.2 M Na/K tartrate
Crystal Properties Matthews coefficient Solvent content 3.93 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.583 α = 90 b = 111.738 β = 90 c = 75.37 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 MARMOSAIC 300 mm CCD 2010-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 50 99.6 0.072 17.6 6.2 17684 17684
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 2.4 2.49 99.2 0.99 2 6.4
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 1IJY 2.4 50 16764 907 99.31 0.2274 0.22605 0.2259 0.25521 0.2551 RANDOM 65.243
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] 0.21 -1 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.805 r_dihedral_angle_3_deg 20.117 r_dihedral_angle_4_deg 18.373 r_long_range_B_refined 13.266 r_mcangle_it 6.044 r_dihedral_angle_1_deg 5.524 r_scbond_it 5.361 r_mcbond_it 3.817 r_angle_refined_deg 1.819 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.805 r_dihedral_angle_3_deg 20.117 r_dihedral_angle_4_deg 18.373 r_long_range_B_refined 13.266 r_mcangle_it 6.044 r_dihedral_angle_1_deg 5.524 r_scbond_it 5.361 r_mcbond_it 3.817 r_angle_refined_deg 1.819 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1877 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing