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Crystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (WRRTTWV)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H3M PDB Entry: 2H3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 292 0.1 M Sodium Acetate, 2 M sodium formate, pH 4.6, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.89 57.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.591 α = 90 b = 51.591 β = 90 c = 88.262 γ = 120
Symmetry Space Group P 31 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 QUANTUM 210 2004-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 99.8 0.059 29.8 5.8 9658
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 0.31 4.7 5.5 930
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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: 2H3M 2 40 9647 9629 458 99.84 0.21 0.21 0.209 0.2131 0.225 0.2358 RANDOM 52.385
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] 1.79 0.89 1.79 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.87 r_dihedral_angle_4_deg 12.162 r_dihedral_angle_3_deg 12.045 r_dihedral_angle_1_deg 5.624 r_scangle_it 3.112 r_scbond_it 1.928 r_angle_refined_deg 1.16 r_mcangle_it 1.033 r_mcbond_it 0.684 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.87 r_dihedral_angle_4_deg 12.162 r_dihedral_angle_3_deg 12.045 r_dihedral_angle_1_deg 5.624 r_scangle_it 3.112 r_scbond_it 1.928 r_angle_refined_deg 1.16 r_mcangle_it 1.033 r_mcbond_it 0.684 r_nbtor_refined 0.297 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.13 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.084 r_symmetry_hbond_refined 0.057 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 825 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction