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Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 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 6.8 SITTING DROP WITH 0.1 M HEPES, PH 6.8, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, AND 0.2 MGSO4
Crystal Properties Matthews coefficient Solvent content 2.5 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.337 α = 90 b = 54.441 β = 98.65 c = 50.219 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 2002-08-31 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 1.85 50 97.4 0.049 25.8 3.57 46421
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 1.85 1.92 83.7 0.413 2.86
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 1.85 49.39 12001 985 97.3 0.175 0.2106 0.226 0.2494 RANDOM 16.42
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] 1.05 -0.68 0.44 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.762 r_scangle_it 5.005 r_scbond_it 3.16 r_mcangle_it 2.005 r_angle_refined_deg 1.815 r_mcbond_it 1.12 r_angle_other_deg 0.941 r_symmetry_vdw_refined 0.668 r_symmetry_vdw_other 0.366 r_nbd_other 0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.762 r_scangle_it 5.005 r_scbond_it 3.16 r_mcangle_it 2.005 r_angle_refined_deg 1.815 r_mcbond_it 1.12 r_angle_other_deg 0.941 r_symmetry_vdw_refined 0.668 r_symmetry_vdw_other 0.366 r_nbd_other 0.257 r_symmetry_hbond_refined 0.251 r_xyhbond_nbd_refined 0.247 r_nbd_refined 0.204 r_chiral_restr 0.113 r_nbtor_other 0.083 r_gen_planes_other 0.015 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 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 1212 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing