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14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and non-canonical binding motifs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M HEPES pH 7.7
0.19 M CaCl2
5% glycerol
27 % PEG400
Crystal Properties Matthews coefficient Solvent content 2.08 40.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.21 α = 90 b = 112.06 β = 90 c = 62.61 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 PIXEL DECTRIS EIGER2 XE 16M 2019-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.911650 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.2 45.52 95.8 1 19.82 13.4 86519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.3 0.854
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3mhr 1.2 45.516 86512 4326 95.83 0.163 0.1618 0.1836 0.1814 17.766
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] 1.056 -0.366 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_3_deg 13.911 r_lrange_it 5.557 r_lrange_other 5.538 r_dihedral_angle_1_deg 5.419 r_scangle_it 3.529 r_scangle_other 3.529 r_mcangle_it 2.36 r_mcangle_other 2.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_3_deg 13.911 r_lrange_it 5.557 r_lrange_other 5.538 r_dihedral_angle_1_deg 5.419 r_scangle_it 3.529 r_scangle_other 3.529 r_mcangle_it 2.36 r_mcangle_other 2.359 r_scbond_it 2.34 r_scbond_other 2.339 r_angle_refined_deg 1.876 r_angle_other_deg 1.584 r_mcbond_it 1.503 r_mcbond_other 1.503 r_symmetry_xyhbond_nbd_other 0.344 r_symmetry_xyhbond_nbd_refined 0.34 r_symmetry_nbd_refined 0.314 r_nbd_refined 0.26 r_nbd_other 0.254 r_xyhbond_nbd_refined 0.224 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.165 r_symmetry_metal_ion_refined 0.161 r_chiral_restr 0.104 r_metal_ion_refined 0.1 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1946 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 5
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement