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Crystal structure of the PDZ tandem of human syntenin in complex with TNEFYF 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 2.3 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.207 α = 90 b = 72.207 β = 90 c = 126.046 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 2003-09-10 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 1.56 30 100 0.063 39.93 9.9 48061
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 1.56 1.63 99.9 0.525 4.25 9.43
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1N99 1.56 63.25 47197 989 100 0.172 0.171 0.201 0.2131 RANDOM 19.65
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] -0.26 -0.26 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.199 r_scangle_it 5.332 r_scbond_it 3.681 r_mcangle_it 2.541 r_mcbond_it 1.637 r_angle_refined_deg 1.494 r_angle_other_deg 0.842 r_symmetry_vdw_other 0.319 r_symmetry_hbond_refined 0.266 r_nbd_other 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.199 r_scangle_it 5.332 r_scbond_it 3.681 r_mcangle_it 2.541 r_mcbond_it 1.637 r_angle_refined_deg 1.494 r_angle_other_deg 0.842 r_symmetry_vdw_other 0.319 r_symmetry_hbond_refined 0.266 r_nbd_other 0.26 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.095 r_nbtor_other 0.083 r_bond_refined_d 0.017 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 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 2652 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing