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Crystal structure of the PDZ tandem of syntenin in complex with fragment F13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 100 mM Sodium Acetate pH 4.6, 200mM Ammonium Acetate, 22% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.23 α = 93.99 b = 57.512 β = 96.08 c = 101.094 γ = 107.7
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 PILATUS3 6M 2017-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 50.02 96.78 0.069 0.08199 0.04369 0.997 9.74 3.5 106108 30520
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 2.2 2.279 95.92 0.3676 0.4347 0.2293 0.925 3.02 3.5 10728
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 50.02 29031 1497 96.89 0.26105 0.25901 0.2631 0.30141 0.3026 RANDOM 46.873
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] 1.07 0.04 0.36 1.05 -1.02 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.186 r_dihedral_angle_4_deg 23.972 r_dihedral_angle_3_deg 16.652 r_dihedral_angle_1_deg 7.052 r_long_range_B_refined 5.37 r_long_range_B_other 5.37 r_scangle_other 1.787 r_angle_refined_deg 1.652 r_mcangle_it 1.569 r_mcangle_other 1.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.186 r_dihedral_angle_4_deg 23.972 r_dihedral_angle_3_deg 16.652 r_dihedral_angle_1_deg 7.052 r_long_range_B_refined 5.37 r_long_range_B_other 5.37 r_scangle_other 1.787 r_angle_refined_deg 1.652 r_mcangle_it 1.569 r_mcangle_other 1.564 r_angle_other_deg 1.239 r_scbond_it 1.087 r_scbond_other 1.087 r_mcbond_it 0.943 r_mcbond_other 0.932 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 4949 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing