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INADL PDZ3 in Complex with a Phage-Derived Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 292 20% PEG monomethyl ether 5000, 0.1 M bis-tris (pH 6.5), VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.957 α = 90 b = 65.156 β = 101.1 c = 82.543 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 345 mm plate 2007-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 98.4 0.09 17.7 5.1 40881
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 96.8 0.596 2.6 5 3986
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 2iwn 2 20 40875 2057 98.35 0.2038 0.2012 0.2003 0.2526 0.2482 RANDOM 36.154
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 -0.2 -0.21 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.065 r_dihedral_angle_4_deg 16.543 r_dihedral_angle_3_deg 12.408 r_dihedral_angle_1_deg 5.937 r_scangle_it 4.755 r_mcangle_it 4.269 r_mcbond_it 3.652 r_scbond_it 3.593 r_angle_refined_deg 1.416 r_angle_other_deg 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.065 r_dihedral_angle_4_deg 16.543 r_dihedral_angle_3_deg 12.408 r_dihedral_angle_1_deg 5.937 r_scangle_it 4.755 r_mcangle_it 4.269 r_mcbond_it 3.652 r_scbond_it 3.593 r_angle_refined_deg 1.416 r_angle_other_deg 0.94 r_mcbond_other 0.786 r_symmetry_vdw_other 0.253 r_nbd_other 0.205 r_symmetry_hbond_refined 0.198 r_nbd_refined 0.188 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.122 r_chiral_restr 0.087 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4391 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 24
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction PHASER phasing