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Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from monomeric fraction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other unpublished model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES, pH=6.5
0.1 M NaCl
0.1 M Li2SO4
23 % PEG400
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.583 α = 90 b = 60.181 β = 117.71 c = 66.292 γ = 90
Symmetry Space Group P 1 21 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 2015-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.928190 Diamond I04-1
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 1.99 42.02 99 0.064 17.3 6.8 29398
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 1.99 2.06 0.636 2.5 6.6 2884
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished model 1.99 42.02 27828 1561 99.12 0.1963 0.19351 0.1957 0.24552 0.2473 RANDOM 36.899
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] 15.28 8.21 10.18 -25.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.48 r_dihedral_angle_3_deg 17.494 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_1_deg 7.126 r_long_range_B_refined 3.973 r_long_range_B_other 3.972 r_scangle_other 2.372 r_mcangle_it 2.36 r_mcangle_other 2.36 r_angle_refined_deg 1.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.48 r_dihedral_angle_3_deg 17.494 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_1_deg 7.126 r_long_range_B_refined 3.973 r_long_range_B_other 3.972 r_scangle_other 2.372 r_mcangle_it 2.36 r_mcangle_other 2.36 r_angle_refined_deg 1.743 r_scbond_it 1.506 r_scbond_other 1.496 r_mcbond_it 1.491 r_mcbond_other 1.484 r_angle_other_deg 1.046 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2993 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing