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Crystal structure of the complex of the PDZ tandem of syntenin with an interleukin 5 receptor alpha peptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N99 PDB ENTRY 1N99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 SITTING DROP WITH 0.2 M SODIUM ACETATE, PH 4.6 28% PEG4000, 0.2 M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.2 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.485 α = 90 b = 48.172 β = 120.24 c = 74.996 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 CCD ADSC CCD 2002-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B NSLS X9B
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 1.7 50 95.7 0.044 25.4 3.4 112090
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 1.7 1.76 72.4 0.287 3.13
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1N99 1.7 64.55 32205 1048 95.8 0.148 0.1613 0.213 0.2213 RANDOM 12.64
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] -0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.059 r_scangle_it 4.302 r_scbond_it 2.72 r_mcangle_it 1.932 r_angle_refined_deg 1.507 r_mcbond_it 1.153 r_angle_other_deg 0.807 r_symmetry_vdw_other 0.308 r_nbd_other 0.254 r_nbd_refined 0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.059 r_scangle_it 4.302 r_scbond_it 2.72 r_mcangle_it 1.932 r_angle_refined_deg 1.507 r_mcbond_it 1.153 r_angle_other_deg 0.807 r_symmetry_vdw_other 0.308 r_nbd_other 0.254 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.203 r_symmetry_hbond_refined 0.17 r_symmetry_vdw_refined 0.151 r_chiral_restr 0.089 r_nbtor_other 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2522 Nucleic Acid Atoms Solvent Atoms 658 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing