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Crystal structure of the PDZ tandem of human syntenin with syndecan peptide
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 20% PEG 3350, 0.2M NH4Cl, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.3 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.322 α = 90 b = 72.322 β = 90 c = 125.921 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 QUANTUM 4 2003-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.97960 NSLS X8C
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 40 99 0.07 30.3 8.3 23083 25.7
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 2.07 100 0.283 8.31 7.9 2282
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1N99 2.3 40 15391 800 99.28 0.197 0.193 0.2053 0.273 0.2927 RANDOM 25.247
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] -0.53 -0.53 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.271 r_dihedral_angle_4_deg 22.434 r_dihedral_angle_3_deg 14.39 r_dihedral_angle_1_deg 5.735 r_angle_refined_deg 2.613 r_scangle_it 2.246 r_angle_other_deg 1.484 r_scbond_it 1.477 r_mcbond_it 1.022 r_mcangle_it 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.271 r_dihedral_angle_4_deg 22.434 r_dihedral_angle_3_deg 14.39 r_dihedral_angle_1_deg 5.735 r_angle_refined_deg 2.613 r_scangle_it 2.246 r_angle_other_deg 1.484 r_scbond_it 1.477 r_mcbond_it 1.022 r_mcangle_it 0.928 r_symmetry_hbond_refined 0.274 r_symmetry_vdw_other 0.211 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.175 r_nbd_other 0.174 r_nbtor_refined 0.159 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.096 r_mcbond_other 0.093 r_nbtor_other 0.085 r_xyhbond_nbd_other 0.015 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2580 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing