☰ Navigation Tabs
Crystal structure of the PDZ tandem of human syntenin in complex with TNEYYV 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 7.5 20% PEG3350, 0.2M NH4CL, VAPOR DIFFUSION, SITTING DROP, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.5 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.134 α = 90 b = 72.134 β = 90 c = 126.221 γ = 90
Symmetry Space Group P 41 21 2
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 2004-02-16 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 2.25 50 99.2 0.066 29.3 5.8 16413
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 2.25 2.33 99.4 0.356 6.4 5.9
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 (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 2.25 8 15024 945 99.6 0.218 0.214 0.2236 0.281 0.2867 RANDOM 29.26
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] -0.43 -0.43 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.333 r_scangle_it 2.457 r_scbond_it 1.399 r_mcangle_it 1.202 r_angle_refined_deg 1.2 r_angle_other_deg 0.783 r_mcbond_it 0.647 r_symmetry_vdw_other 0.241 r_nbd_other 0.23 r_xyhbond_nbd_refined 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.333 r_scangle_it 2.457 r_scbond_it 1.399 r_mcangle_it 1.202 r_angle_refined_deg 1.2 r_angle_other_deg 0.783 r_mcbond_it 0.647 r_symmetry_vdw_other 0.241 r_nbd_other 0.23 r_xyhbond_nbd_refined 0.211 r_symmetry_hbond_refined 0.198 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.111 r_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 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 2590 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing