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Crystal structure of the PDZ tandem of syntenin in complex with fragment E5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 100mM Sodium Acetate
200mM Ammonium acetate
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.114 α = 82.71 b = 56.13 β = 83.462 c = 102.867 γ = 77.033
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 2017-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.76 27.63 97.29 0.1388 0.08908 5.27 5.27 15909
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.859 96.74 0.4417 0.288 2.26
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1N99 2.76 27.63 15823 782 98.006 0.277 0.2746 0.2662 0.3171 0.3076 50.548
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] 7.622 -1.163 -0.676 -2.241 2.756 -5.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.276 r_dihedral_angle_6_deg 11.576 r_dihedral_angle_2_deg 10.986 r_dihedral_angle_1_deg 6.24 r_lrange_it 5.777 r_lrange_other 5.744 r_mcangle_it 2.538 r_mcangle_other 2.538 r_scangle_it 2.07 r_scangle_other 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.276 r_dihedral_angle_6_deg 11.576 r_dihedral_angle_2_deg 10.986 r_dihedral_angle_1_deg 6.24 r_lrange_it 5.777 r_lrange_other 5.744 r_mcangle_it 2.538 r_mcangle_other 2.538 r_scangle_it 2.07 r_scangle_other 2.07 r_mcbond_it 1.432 r_mcbond_other 1.432 r_scbond_it 1.142 r_scbond_other 1.141 r_angle_refined_deg 0.737 r_angle_other_deg 0.294 r_nbd_refined 0.18 r_symmetry_nbd_other 0.177 r_symmetry_nbd_refined 0.171 r_nbd_other 0.159 r_nbtor_refined 0.155 r_ncsr_local_group_4 0.131 r_xyhbond_nbd_refined 0.13 r_ncsr_local_group_5 0.123 r_ncsr_local_group_2 0.12 r_ncsr_local_group_3 0.117 r_ncsr_local_group_1 0.114 r_ncsr_local_group_6 0.11 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_xyhbond_nbd_other 0.103 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.036 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4928 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing