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The complex structure of syntenin-1 PDZ domain with c-terminal extension
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 M TRIS HYDROCHLORIDE (PH 8.5), 30% (W/V) POLYETHYLENE GLYCOL 4000
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.525 α = 90 b = 88.529 β = 90 c = 90.368 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) PAL/PLS 5C (4A)
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 2.8 50 97.6 0.07 24 8.8 13799 0.2
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 2.8 2.85 93.9 0.29 4.36 4.8
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 2.81 50 12615 667 96.35 0.19624 0.19426 0.2209 0.23493 0.2549 RANDOM 37.641
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] -0.21 -0.39 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.019 r_dihedral_angle_3_deg 22.063 r_dihedral_angle_4_deg 21.78 r_scangle_it 8.231 r_dihedral_angle_1_deg 7.695 r_scbond_it 5.677 r_mcangle_it 5.618 r_mcbond_it 3.34 r_angle_refined_deg 2.269 r_nbtor_refined 0.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.019 r_dihedral_angle_3_deg 22.063 r_dihedral_angle_4_deg 21.78 r_scangle_it 8.231 r_dihedral_angle_1_deg 7.695 r_scbond_it 5.677 r_mcangle_it 5.618 r_mcbond_it 3.34 r_angle_refined_deg 2.269 r_nbtor_refined 0.342 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.207 r_chiral_restr 0.142 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.057 r_bond_refined_d 0.027 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2687 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing