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Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from dimeric 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Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other unpublished model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 293 0.1 M MES
0.1 M NaCl
0.1 M Li2SO4
22-26% PEG400
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.671 α = 90 b = 60.174 β = 117.62 c = 66.128 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 1.88 41.98 99 0.085 13.1 6.9 34407
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 1.88 1.96 0.963 1.8 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished model 1.88 41.98 32604 1809 98.36 0.18641 0.18468 0.21702 0.2231 RANDOM 33.046
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] 0.38 0.85 11.53 -11.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.246 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_3_deg 14.748 r_dihedral_angle_1_deg 6.258 r_long_range_B_other 4.768 r_long_range_B_refined 4.766 r_scangle_other 3.053 r_mcangle_it 2.269 r_mcangle_other 2.268 r_scbond_it 1.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.246 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_3_deg 14.748 r_dihedral_angle_1_deg 6.258 r_long_range_B_other 4.768 r_long_range_B_refined 4.766 r_scangle_other 3.053 r_mcangle_it 2.269 r_mcangle_other 2.268 r_scbond_it 1.933 r_scbond_other 1.914 r_angle_refined_deg 1.591 r_mcbond_it 1.482 r_mcbond_other 1.482 r_angle_other_deg 1.002 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 2996 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Aimless data scaling