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Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G4X 5G4X, 4DXA experimental model PDB 4DXA 5G4X, 4DXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 289 0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.032 α = 90 b = 54.107 β = 109.51 c = 203.11 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2018-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97918 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.81 50 94 0.15 0.164 0.065 4.2 6.1 40063
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.81 2.86 85.4 0.948 1.042 0.421 0.757 5.6
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 5G4X, 4DXA 2.82 49 38087 1976 93.3 0.2433 0.2403 0.2411 0.2998 0.2969 RANDOM 66.375
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] -2.81 -1.72 8.87 -3.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.909 r_dihedral_angle_3_deg 22.416 r_dihedral_angle_4_deg 21.204 r_dihedral_angle_1_deg 5.698 r_angle_refined_deg 1.483 r_angle_other_deg 1.201 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.909 r_dihedral_angle_3_deg 22.416 r_dihedral_angle_4_deg 21.204 r_dihedral_angle_1_deg 5.698 r_angle_refined_deg 1.483 r_angle_other_deg 1.201 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10982 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction